Problems after switching 99 engine/trans in 98

[dbcscanada]

As the title indicates, I've switched the engine & trans from a '99 into my '98. The problem(s) I'm encountering is that the trans is shifting very harshly between gears. It never did this with the old engine. Any ideas?

The computer was NOT changed when the engine/trans was changed. Could this be a problem?

A supposed trans expert, suggested the TPS was not acting properly and the old TPS was taken from my old engine and placed on the "new" one... no difference is shifting quality.

Two alarming features have manifested themselves:
Firstly, under hard acceleration, the shift from 2nd to 3rd occurs at about 3500-4000 RPM and then drops back to 2nd when RPM reaches about 4500 and will then shift at redline into 3rd. The previously mentioned "harsh" shift occurs under hard acceleration...
Secondly, and not always, but this has occured under normal acceleration where the trans seems to shift into neutral and redlines when in 2nd gear. This, needless to say, is very concerning, as it requires a bit of quick reflex to get off of the throttle when this occurs.

I understand that the trans is controlled by "wire" and not mechanically controlled, but does anyone have any ideas as to what I should be doing to fix these problems?

Tanks in advance,

[dbcscanada]

Follow up:

I changed the computer from the 99 engine/trans with the 98 and THAT made the difference! The trans is now shifting as it is suppose to and I haven't had any wild RPM occurences.

I guess that engine swaps should include as much hardware from the new, if years aren't the same...

Best regards,