Help with diagnosis..

Toast

This is a 10% whole grain rye, with 1.25% (fresh) yeast and everything seemed to go well until baking, the dough developed nicely and was easy to shape, but it didn't rise much in the oven and crumb is kind of closed. I'm not sure if it was underproofed and/or overproofed or just bad shaping? I haven't baked with fresh yeast in a while, typically use sourdough so I wasn't really sure about the timings. 

I mixed everything, let it autolyse about 30 min, bulk ferment about 4.5h, 30min bench rest, shape and then final proofed for about 1h. 

Taste was actually quite decent, but I wanted it to be slightly more open.. 

Yes I mixed everything at once except salt, autolyse for ~30min and then add the salt, do some folds in the bowl for a few minutes, let it rest a few minutes and come back and so on until I feel the dough has developed enough. I did a few folds during bulk ferment as well, probably about 3.

Sounds good to me. I think for an open crumb you'd be looking at getting the optimal bulk ferment, handling correctly, shaping and judging the final proof well. 

When doing the stretch and folds try not to knock the air out. Don't over tighten the dough. 

Bulk ferment is done when it's aerated, billowy, there are visible signs of bubbles just beneath the surface and the dough is silky smooth. 

When shaping do a pre-shape, rest for 15-20 minutes, then final shape. 

Knock the big bubbles out but do not de-gas. 

Final proof till just under doubled. 

You only need small tweaks here and there as that is in itself a lovely loaf. 

...10% rye/90% white is one of my standard bakes.  From the info provided, I would go with a proofing problem - what white flour do you use?