Just finished up with my n20 install and when I was leaving the shop, I tried taking the car, (not while spraying thank goodness) past 4000 rpms in 5th gear and it wouldnt It felt like it was misfiring and felt like that was where the fuel cut/rev limiter was set to. The shop that did the install tapped the ecu when they wired the window switech (62 for throttle and 50 for tps). The car drives fine up to 4k because I drove 160 miles home after the install.

My ideas of sources of the proplem: 1) tapping the ecu 2) removing the intake tube (messed up the maf/throttlebody)

What could be the issues??

 

The things that you have already stated and a "lean cut" as well

 

I found out the problem was the window switch; it was spraying fuel whenever the rpms reached the set activation point. By 4000 there was so much fuel that the ecu wouldnt let it rev past 4000.