One strategy I am exploring right now is to do the rough-in of the entire project (i.e. get the electrical, plumbing, framing, etc done).

Should I plan on handling specific repairs (roofing, electrical wiring, plumbing) on my own with contractors and then hire a GC to handle the rest (painting, kitchen & bathroom remodel, flooring, etc.)?

In addition to bringing the plumbing, electric, and HVAC up to code, I also removed a wall between the kitchen and living room, expanded the bathroom, replaced the remaining old windows, repaired stucco, rebuilt the entry steps, replaced all lighting fixtures, refinished all hardwood floors, and repainted.

Roof sagging, code issues, plumbing problems and cracked hvac, among other stuff.

Blatant things like venting the furnace into the attic, substandard wiring, plumbing venting not connected, etc.  

I have used his plumbing company for years as a sub on our properties and he has good cash flow and is consistently honest.   

The condo I have is a 1BR / 1 bath with a unit next door in far worse condition (unit I acquired did a complete rehab - new kitchen, baths, plumbing, heating, electrical and windows) is under agreement for asking price of $129k.

Is putting lipstick on a pig something like just replacing carpet and painting in a house that needs electrical ,plumbing ,or foundational work?

They had it inspected the next day, and relayed some concerns about the roof and plumbing, which is a segue to a repair amendment that's going to cost more money.  

We could do the same for replacing the plumbing to pex and pvc.