Try it and see if the car runs better.
The ECU is different between the GT-LX 5.0 cars than it is in the Cobra. The Cobra also came with 24 lb/hr (versus the GT-LX 19lb/hr) injectors IIRC and a different (somewhat larger) MAF meter.
THUS a MAF meter designed for a GT-LX V-8 won't operate well with a Cobra ECU and injectors. You can't switch parts around without tuning. Aftermarket MAF meters typically operate by sending a modified voltage signal to the computer to account for different sized injectors.
Honestly, it gets kind of complicated. Put the stock meter on it and see if the car does what you want. If not, its another problem. If it does, then the aftermarket MAF meter you have is junk (or just not Cobra compatible). The TB shouldn't negatively affect performance.
Edit: You asked how the car would run... It would run either rich or lean, depending on the MAF meter calibration. If its too much of either, it will run like poop. If its rich, it'll smoke a lot. If its lean, it'll get really hot and you run the risk of destroying the engine itself.