The reason that was question #1 is because that is WAAYYYYYYYY too much gear for an M5R2. It may be the cause of your issue, but even if it isn't, it is still an issue that you should fix. 1st gear in your transmission is 3.75. To put that in perspective, a world-class T5 has a 2.97 1st gear, so as far as 1st gear is concerned, any rear end gear behind an M5R2 acts like it is 25% steeper than it would in a Mustang. So imagine putting a set of 5.13s in a fox body Mustang and trying to drive it on the street. If you have 4.10s, that is effectively what you are doing, and 1st gear is completely useless. 3.27s or possibly 3.55s is really as far as you want to go with an M5R2 trans. 3.27s came stock in automatic SCs, so you can probably buy a used 3.27 diff for around $150, swap it out, and sell your 4.10 diff to someone for probably $400. This will put some money in your pocket, give you a whole bunch of drivability back in your car, likely actually make your car faster, and also possibly avoid this ever coming up again since with 4.10s at 3800rpm you are going 97mph (fast, but easy to accomplish opening it up on the highway), but with 3.27s 3800rpms would be over 120mph.
Moving onto the CAI. You say you changed the MAF: what MAF did you install? Was the car tuned? Installing a different MAF without tuning it can and likely will throw the fuel curve way off, which can cause all kinds of drivability issues. 3800rpms in 5th is a heavier load on the engine than in 4th or 3rd, so if it is running rich, or worse lean, it may be able to pull past that in the lower gears, but not in 5th.
If the car has always been a 5-speed, then that rules out my other theory. I know some automatic SCs have speed limiters at 120mph, and since 3800rpms with stock gears would have been just over 120mph, I thought maybe the speed limiter was kicking in. The only way this could be the case though would be if you swapped an automatic SC ECM into this one, and even then, I'm not sure it would work that way.
Another possibility is it could be some kind of an ignition fault, possibly a bad crank or cam sensor, or DIS module.
At this point, I would start by swapping the stock MAF and airbox back into the car, since that is the easiest/cheapest thing to do. If the problem still persists, put 3.27s back in the car. If you still have the problem after that, start looking into your ignition system.