Lot's going on here, let me take a stab at it from my POV. Being a commercial roofing estimator in another part of the country.
The roof has been examined by a roofing consultant/engineer AND a GC [my client/friend] and 4 roofers. Two roofers wanted to slap down another layer of BUR, despite the fact that I don't want BUR and the structure can't handle another layer of that stuff [and yes, I don't like it!].
Looking at the photos, Complete tear off down to the deck. No question. The two "roofers" are a joke.
Get rid of the BUR, use 2" poly-iso rigid insulation sandwiched between SecureRock or DensDeck prime. Copper skylight can stay, it needs a new curb & flashings. Biggest issue? A curb needs to be built between my unit and guy nextdoor, as the demising curb btween units has been layered in BUR so much, it's disappeared [see photos].
You might think about using 2.5" iso and a coverboard. Additional "R" value to meet IBC code (R-20) for re-roofing.
I actually think your "biggest" issue may be the masonry under all that flood coating. That chimmney looks like it has had a lot of moisture trapped against it and the mortar and bricks area deteriorating.
There'll be very little to adhere to without repairs.
No telling what the parapet walls look like until the flashings are gone.
I've spoken AT LENGTH to the manufacturer's reps for Fibertite & my asst spoke to the Durolast rep, who even came out to the site. For reasons I don't understand, and my GC client doesn't get [he even intervened and got on the phone and called the Fibertite contractor who has done work for them recently!] - this small project isn't interesting.
Talking to Manufacturers Reps is usually an excercise in futility. All they want is the BIG stuff.
Here's my take on your job....
Before the roofing starts, have the parapet walls and that chimmney looked at, My fear is as stated above. The flashings can be peeled away for inspection and temped back in.
Without at least an idea of what's going on under all that asphalt the roofers will open it up and find nothing but dust for walls. Without a masonry restoration contractor lined up, that's a costly delay and a real problem.
Coordination is key between the two. Remove only as much flashing to expose the walls that then can be repaired in a day. No open roofs EVER!
My recommendation... Tear it off completly.
Screw a layer of 2.5 iso, hot mop a 3/4" layer of perlite over that, mop a 43# base sheet.
Heat weld a 160 mil modified bitumen membrane preferably derbigum GP. This is NOT rolled roofing. Or available at Home Depot.
New blocking at the perimeter with a cant where needed.
New 24 ga galvanized prefinished edge metal. New 24 ga galvanized prefinished counter flashings along all wall flashings.
Raise all curbs to a minimum of 8" above the finished roof level. Eliminate the ones not being used.
Replace all vent stack leads.
New sumped drain leads installed.
Replace that skylight. It may look nice but, I guarantee that glass will begin cracking and leak. A new unit will perfrom much better and save you heating dollars in the long run.
I cannot give you a hard number for the job, I would need the following:
Total square footage of all areas, lineal footage of the flashings including height, That includes curbs, walls, parapet caps.
How much tear off? In other words, what is the thickness of the existing roofing materials. and what types. (has anyone done core cuts to verify the existing?)
Be sure to build in a contingency for deck replacement if needed. Usually a square foot price for time and materials as it is completed.
That should be included in the roofers proposal.
A square foot price for the job in our area using the system described above would be between about $5.50 - $7.00 a sqft.
We have our own dumpsters and boom trucks. We crane the tear off from the roof and haul it away.
Another question I have is what is your objection to a BUR?
A properly maintained BUR WILL outlast any single ply on the market. In addition, with a single ply, that's all you have between the weather and your computers! a single thin layer.
.45-.60 mils of plastic or rubber. cut or hole and the waters in.
OR a minimum of 160 mils and a base sheet with Mod Bit OR 250 mils of 4 ply and asphalt. built in redundancy .
Also be wary of a manufacturer that calls it's product the worlds best roof!
Just my $.02 worth.