Help with simple bread baking recipe

Sounds like a nice recipe! You say at the beginning that you've gotten it to a point that you like, so I would only tweak things if you are looking to change the results.  (Ingredients and method are ways to get what you want, right?). It sounds like the things you may still want to play with are crust and crumb density.  I'm not an expert on these things, but 100% Whole Wheat is always denser and crustier in my bakes.  I'll let more experienced Whole Wheaters weigh in on what you might do if you are looking for a thinner crust or a lighter crumb.  Good luck! 

First off, I have to say that I have no familiarity with any of the specific ingredients you’ve listed.  I have also never worked with a 100% whole meal flour recipe.  Since you have not listed the specific recipe you are using, it is difficult to say what, if any, of the processes you are using are not working as the recipe intends.  Most recipes list not only the ingredients needed, but also the specific list of steps, in a specific order, which should be followed to produce the desired final product.  Keep in mind that even the smallest change to a recipe can have unintended and undesired effects on the finished product.  When making changes to a recipe, you should make small changes, one at a time, in order to be able to pinpoint which changes worked and which changes did not.  This will require a great deal of trial & error.  It’s also worth noting that some changes will necessitate other changes to be made (e.g. different flours will require different hydration levels; increasing proofing temperature will decrease proofing time; etc.)

The following are only suggestions, based upon your questions along with the information you provided.  This is by no means a complete and comprehensive list of things that may improve your final product.

1. Kneading:  I would try to add some kneading into your process.  Kneading helps develop your gluten network, which in turn is going to help get some rise in your finished product.  This will help alleviate some of the denseness.  The yeast you are using may allow you to skip a second rise, but it plays no part in gluten formation.  Gluten is created by mixing flour and water.  Kneading takes the gluten (which form together as long strands of protein molecules), and stretches it into a matrix that is capable of capturing and holding small pockets of CO2, which are basically the waste products created as the yeasts ferment the sugars/starches present in the flour.
2. Mixing:  I would discourage you from mixing the water, yeast, and salt without the flour.  This can actually kill some (if not all) of the yeast before it has a chance to really do its thing.  There are a couple different ways you can mix these ingredients safely, and finding which works best will take some trial and error.  A) You can mix the water & yeast (allow it to sit a few minutes in order to let the yeast become active) and in a separate bowl mix the flour and salt.  Then slowly incorporate the two together.  B)  you can mix the water & flour (saving back a small amount of the water).  Allow the water and flour to sit for 1/2 to 1 hour, in order to fully hydrate the flour and allow some gluten to develop.  Then mix in the yeast, dissolved in a bit of water, then mix in the salt, also with a splash of water.  C)  Mix the water, flour & yeast, allow to sit for 10-15 minutes, then mix in the salt, with a splash of water to help it dissolve.  
3. Second rise:  the addition or removal of a second rise will change the finished product in some way.  The only way to know for sure is to try it both ways, and see which you prefer.  The yeast you are using claims to not need a second rise.  Admittedly, I have never used this yeast, so have no familiarity with its peculiarities.
4. Proofing temperature:  the answer to this is going to depend on the ambient temperature in your kitchen.  If your kitchen is around 75f - 80f (24c - 27c) then you should be fine to poof at room temp.  If your ambient temperature is cooler than that, you can either proof for a longer trip me, or find a warmer location for proofing.  The bowl of hot water trick is not a bad idea, as it will increase the temperature in your oven and also increase the humidity, but it will also drop in temperature over time as the water cools off.  As for your other oven trick, turning it on for 2-3 minutes is likely to make it hot enough to kill your yeast.  If I turn mine on for 15 seconds, I wind up with temperatures just above 100f (38c).  It might be worth trying this: park your proofing dough in your cool oven, and turn on the oven light.  This can usually provide enough increase in ambient temperature (my oven with the light on reaches about 95f (35c)).  You might even consider mixing these two (oven light + hot water bowl).  No matter what you try, invest in a decent probe thermometer to monitor these temperatures to keep from killing off your yeast.  Also worth noting:  your proof times will need to be adjusted when tinkering with your proof temperatures.
5. Bread density:  The density of your finished product will be affected by both your ingredients and your technique.  Substituting some all purpose flour for a portion of your whole meal flour may help with this (although different doughs absorb water at different rates, so substitutions may also require tweaking the amount of hydration used).  As mentioned above, some kneading should also help with the density, as will making sure your yeast stays alive long enough to do its job.  The hardness/crustiness of your rolls is also greatly affected by these things, as well as the overall hydration level.

Welcome to the delicious process of making bread but be careful as it is addictive!  Also,congratulations on finding a simple recipe to start with.Any ideas you use will only improve the outcome. The trick is to not lose track of what you did so take notes and change only 1 thing at a time. You are at the very beginning of a bit of a learning curve.

First of all, in regards to kneading. Kneading with WW (wholemeal or whole wheat) will help to hydrate the flour particles,develop the starch and help form a nice windowpane.(I will put good search words in italics). This helps the dough to trap the gas that forms the bubbles and is very beneficial for a nice crumb. The rolls may be less dense since the gas is trapped instead of escaping. WW rolls will always be denser that AP flour rolls but do not have to be rocks. Adding a little oil/fat may help with that also.

Along with alllowing the flour to have enough moisture is the very important step of allowing the flour and bran bits the TIME to absorb the flour. Adding a simple autolyse,sponge, or soak is very important to the quality of a WW crumb. If the branny bits are not given some time to absorb the moisture before the bake, then after the roll is baked they will continue to absorb the moisture from the crumb and the roll becomes very crumbly as you bite into it. The autolyse does not have to be elaborate or very long-30-45 minutes of sitting on the counter after a preliminary mix.

Autolyse can become elaborate and even include a cold retard where the dough is mixed and then refrigerated for a period of time before baking-done at any stage-bulk fermentation, shaped,proofed. I have a favorite WW recipe that uses a starter and the dough is mixed and kneaded in the evening and put into a large container in the refrigerator overnight. It can go in quite moist and sticky but by the next am is soft and slightly tacky (if I get the hydration correct). The next morning I let it warm up, shape and bake. Loaves with a long soak and good windowpane are softer and fluffier.

I have very successfully done "dump" mixes where all dry and all wet mixed in separate bowls and then mixed together. Bread is very forgiving. Can it be "better" if you do it differently? Maybe. But if it works out well for you, do what works for you.

There are some practical responses to some advice:

"Put it into a slightly warmed oven to raise" I have forgotten several times (or my spouse) and turned the oven on duriing a proof-disaster!

"Don't add salt til the end of a mix-salt kills yeast and you get a better windowpane and crumb"  True, but I have frequently forgotten to add salt and had gorgeous, bland loaves. I'd rather add salt and get slightly less gorgeous,delicious loaves.

You will get TONS of advice-some of it may seem conflicting but just addresses different ways of accomplishing the same end- a delicious,WW roll. Choose what you want to do (or don't want to do), experiment by changing only 1 thing per bake and keep notes. After the next 4-6 bakes you will figure out what works for you.

So do a little reading and bake some deliciousness!

(I have responded often to the WW posts if you want to search for me in the search box.A great  poster is txfarmer-she had some beautiful bakes and dabrownman has great posts along with drooling pics)

If you want them to rise slower and develop a bit more flavor, you can reduce the amount of yeast. Try 3/4-1 tsp of yeast and see if that slows that rise down enough and still allows a workable timeframe.

If after shaping, the rolls overproof you can reshape and rise again as most of the recipes using commercial yeast of any kind have plenty of rising power. Unless they are flat and getting wet-that dough is too far gone to make anything except pancakes.

A little fat added may tenderize the crust a bit-1-2 tbsp oil/butter/lard.

Remember...do 1 change at a time and keep track.

Those rolls looked much better than the original.

I can see where you fingepoked the rolls and do have a comment on that. If anything the rolls may be sllghtly overproofed. Proof checking is (for me) the hardest thing to determine but as long as you get it close, you're fine.

If you poke your finger lightly into the dough and it bounces back strongly, that means the dough is not quite ready. It demonstrates that the gluten strands have not relaxed sufficiently to stretch and spring when the dough hits the heat of the oven. When it hits the oven heat, it will rise a little bit and bake but have a dense crumb as the gluten strands held together tightly before the heat set them in place.

If you poke your fiinger in lightly and there is no resistance and the indent stays, that means the dough is overproofed. The indent has popped the bubbles under the finger and there is no bounce for the dough to spring back. When it hits the heat of the oven, it will puff up and fall as the walls of the bubbles are too stretchy and too weak and the bubbles pop. A dense crumb again but for a different reason.  Might be best to reshape the dough and proof again. Modernist Bread author has stated this is possible to do 3-5 times when commercial yeast is used but probably not for natural levain.

If you poke your finger in lightly with just a  little resistance and the indent fills in more than halfway-it should be perfect.The gluten strands are relaxed enough to not pop bubbles when poked and strong enough to spring back. In the oven heat, there should be a good spring and bubble expansion before it is set.

Have fun!