Throttle lag or trans issue?????

I have the same car and have not experienced any problem as you state. Watch the tach and see when the shift is actually made. If you tach to high you will hit the rev limiter. That will make you fall flat on your face. Does it work ok with it auto shifting?

I have a CAI and tune but neither before or after that being installed have I had any problems.

Get a CAI/tune package from either Brenspeed(where I got mine)or Bamachips and that will totally disappear! With the tune, you can select different shift pressures(up to 25% over stock in 5% increments)which makes for some neck jerking tire chirping shifts!

Sounds like AZ Pete may have hit the nail on the head. These cars act differently when hitting the rev limiter than the older mustangs. When I hit rev limiter on the SN95 I had, it would literally bounce off, drop a few hundred RPMs, rev up again, and repeat. When I hit the rev limiter on my new car, its as you described. It just pauses at the rev limit. Also, when manually shifting, the transmission doesn't respond immediately to a gear shift, so consider that when timing things.

I also like Kooldawg's suggestion though!