Hi Jon,
I'll try to answer your questions...
1. Advantage of 5 lug is more options/choices of rims.
2. Running 16" rims is cool, just remember with a bigger rim, generally the more expensive the tire/rim cost.
3. IMHO a brake kit that has been engineered for your truck is better then trying to re-engineer 2 frames together.
4. If 3 is done.. this is not an issue.
5. If 3 is done.. power steering is not an issue.
6. If I understand it correctly... they are the same from the cab doors forward.
7. If the subframe was installed incorrect, they will know right away..... Depending on the "straightness" of the frame, they may or may not be able to do it.
I would rather do the brake kit, someone else has already done the work.... All I have to do is install it

If I have mis-stated anything I hope someone will correct me.