And, it failed on plumbing and electrical ...it wasn't even a close call. 

Once you have an AC compressor stolen or the copper plumbing removed, that deal is much less profitable.

Just as another topic somewhat related, pulling electrical, plumbing, mechanical permitting, does this require a licensed person for each sub contract or can the GC pull any permit required to build?

So, you have different systems and they should be divided in something like this: roofs, exterior, interior, structural, mechanical, plumbing, electrical, to name some). 

No issues with the plumbing, electrical, central A/C, etc.

Some might just have you open up a few holes so they can check the plumbing, etc and others might make you tear everything out.  

Plumbing a 2 bathroom is the same cost in any house. 

New windows, siding, roof, plumbing, electric, HVAC, new well drilled, everything interior/exterior was new.

When you need plumbing, electrical, HVAC service where do they come from and will they charge extra trip charges.

I literally just spent $3k in the past month and a half chasing a plumbing(sewer) problem that I'm still not positive has been fixed completely.