Doesn't sound that out of the ordinary for your mods. That Hotshot header alone is good for at least 2 MPH over stock, and stock you should be running in the 87-88 MPH area. It sounds like your tuneup cleared up some issues you were having, and now you're where you should be.
I also ran a 90 MPH trap speed in my NX2000 with a Hotshot header and intake.
I suggest the next things you get should be a CAI, a JWT ECU and JWT cams. You don't have to get them all at once, but they will ALL add a good amount of HP. ~8 wheel HP for the CAI, ~10 wheel HP for the ECU, and depending on which cams you get, probably over 10 wheel HP for those too. Possibly more. With those 3 mods you can probably net a solid 20 wheel HP over what you have now, especially considering that your car seems to be in excellent running condition right now.