The IRS bolts into any 99-04 car. The only "hackjob" might be the brake lines and if the E brake actually works or not...
"Cobra clutch", he may mean the discontinued "King Cobra" or one of the many current "King Cobra Style" clutches. Truth is that all 01.5-04 GTs got a very good 11" clutch setup just like the Cobra so if that is something the seller is trying to push then ask for a receipt first and also its not really a major selling point.
"Frame ties", I'm assuming you mean subframe connectors. The factory convertible/mach bolt in ones might as well not even be there. If they are full length welded ones that is a good deal. However, to get that done with all new parts/labor is $400 so again... not a huge deal $$$ wise.
"Cobra suspension". Same bleh stock suspension as the GT unless we are talking the 00R (we aren't). Obviously the IRS is different but it still has the terrible wheel gap up front and the stock shocks/struts/springs are only mediocre at best.
You are basically going to be going on condition of this car honestly. We all know what they KBB/NADA for but that is honestly not very representative of one in good shape/low mileage/both. On the other hand, with the mods you listed, it isn't exactly worth very much more than if it didn't have those mods.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.