Sorry KDillon, I forgot about the other questions in your post. First, peppers are a continuously fruiting plant, and will grow fruit all their life. You can use
hps on continuously fruiting plants as soon as you want (their constantly fruiting). It shouldn't slow down the foliage growth much at all. Changing to HPS only changes the light spectrum, and allows the plant to dedicate more energy to the fruit growth/production. So in theory more energy going to the fruit, less energy going to foliage. But I doubt it would be noticeable much. Many people use nothing more than MH on peppers, and others use only HPS.
You can prune as much of the inner leaves as you want. I wouldn't prune any that aren't being bunched up though. If they are being bunched up, they wont be able to grow much anyway, and by getting rid of them you'll be able to get better air circulation through the plant. Just make sure you prune them at a node (where the stem comes out from a branch/leaf). Keep in mind that a flow/pepper typically grows at every junction between leaf and branch. So the more you trim the less flowers/peppers.
The transition stage of
nutrients is fine. If you want the plant to grow more foliage use the directions for the vegetative stage, if you want it to concentrate more on fruiting, use the directions for the blooming/flowering stage. If you want it to do both at the same time, stay right in the middle.