There were shingles, wood, and shingles on top of each other.

He did say it was missing shingles, which it was not last year when we had it checked.

Roof is original (Shingle) $4k is as I expect to have to put in about $1k each unit in some shape as carpet, paint etc? 

I'd have to run sewer and all utilities to it, as well as do a studs down remodel (it actually has good bones and a reletively newer asphalt shingle roof). 

What are the thoughts on shingling over a layer of existing shingles? 

We have T-Lock shingles in our area and they're so prone to failure that insurance companies have stopped insuring them, forcing roof replacements.

My next project is removing a skylight and replacing with shingle roofing - this has just become a necessity for me because I contact a bunch of companies whenever I have a project, most never respond, those that do are either booked up or never show up to give an estimate, etc etc - requires me doing it myself!

Update:According to the inspector, the roof needs to be changed out soon because the shingles are cracked, some spots are showing the foundation that it is glued onto.

No tear off , right over the shingles .  

A 988sf roof w/ a 6/12 pitch is only 1,105 square feet of roofing w/ a 10% material waste that's ~12 squares of shingles.Roof Quantity CalculationOakridge roofing shingles are $140/sq at Lowes.12 squares*$140/square = $1,680 in shingle materials + a few hundred dollars of underlayment and flashings, so there shouldn't be more than $2,000 in materials.So in other words your Contractor has quoted you $9,000 for labor for a roofing job that will likely take a crew of 3-4 guys one to two days tops.