The GM doesn't use an ECT (engine coolant temperature). It uses a CHT (cylinder head temperature) sensor instead.
The Mustang GT uses an ECT and does not use a CHT.
If you were to purchase an intake manifold for a late model GM you MIGHT find the spot for the boss where the ECT is drilled and tapped is NOT be present.
Since the Mustang does use an ECT then what ever replacement intake is used also needs an ECT.
Bottom line. You need to match the ELECTRICAL requirements of the original car. The car's computer is expecting to see the sensors it was born with. The PCM doesn't know (and shouldn't care) that the long block from an 07 GM has been used. Which if all of the electrical wiring and sensors are in place will be true.
I have been asked in other threads about the late model GM and the ECT. The question is "why not just drill and tap the cross over for the an ECT sensor". The problem here is that the extra metal that forms the BOSS has been removed from the casting. Therefore if you were to attempt this, it's likely that there isn't enough metal to support drilling and tapping.
Don't over think this. If you compare side by side the two intake manifolds it will be obvious which manifold has an ECT sensor and which does not.
OBTW, I have done this swap. The motor currently in my 2000 GT originally came from a 2003 Grand Marquis. Since I have over 100K miles on the swapped motor, by an measure the job has to be considered a "success". In fact I have put so many miles on the swapped motor I have had to replace the timing set.
Hey I have a quick question, I def made a mistake with my swap lol. Along with the engine I replaced the transmission too and going off of various forums I read claimed that 99-04 gt's came with the 4r70w. I did see some people say that the 04s came with the 4r75w but I couldn't find anything definitive and I'm kicking myself for not simply calling up my local Ford and confirming what came in my car, which is the 4r75w.
So with that out of the way I'm sure you can guess what problem I'm having. Speedo isn't reading the proper speed, I have a handheld diablosport that's locked to my old mustang that was totalled and I was unable to unmarry it but that's fine as I only use it for live diagnostics and trouble codes. The tuner also showed that the PCM isn't reading the correct speed as well (which is under 10mph, eventhough I'm doing 30mph, which was verified by one of those roadside "your speed" things. That would explain why the needle isn't moving and the car won't shift on it's own out of first, I can manually shift it to second.
So my question is this, would the solution to my problem be either:
1. Find an ECU (or pcm, don't know the proper term but I know what it is) from a 99-03
2. Pay to get my tuner unlocked and change the value that's needed to correctly read the speed being sent from the transmission.
3. Get another 4r75w. I actually know of a good deal on one but I'm not trying to stomach the cost of buying and swapping another transmission out along with trying to find a buyer for the one I have, buying new seals, fluid, etc lol