Okay so very soon I will be in the process of making a 2x2x1 the way Redkb made his (http://www.youtube.com/watch?v=n5-GiKIoGeQ
Reference video) and he using Apoxie Sculpt to fill in the cracks so the pieces look smooth. I don't have Apoxie so i was wondering if I could use Repair Plastic Epoxy and it would work the same?
I haven't heard of that, but if it sticks to the plastic it is probably fine.
Unlike building extensions, the material you use to fill in gaps is pretty forgiving. It needs to stick and be able to be smoothed (likely with sanding). Most will be under stickers but if you want to paint it make sure the paint will stick.
Try a test on a throw away puzzle perhaps.