It really just depends what your final goal is. How low do you want to go? If you want to lay the frame on the ground, then you'll need to do some notching or a "z" in the frame regardless of which suspension you have.
You can keep the beams and get pretty low. The problem with going really low with beams, is that the geometry and the travel kind of sucks. That's why trucks with ibeams have tons of negative camber when they're lowered or aired out. Switching to control arms (Mustang II, newer ranger, or yota clip) gives the suspension better geometry as is moves, reduces camber problems, and may even ride better. But, it's more work, and costs more $$$. It's all about your priorities.
As far as wheels go, you have to think about more than just diameter. The bigger you go, the more work it's going to take to get the truck low. You also have to consider wheel width, offset, and tire sizes too. Again, it's all about your priorities, how much you can spend, and what you want the final result to be.