2000 Pontiac Bonneville
1. Tranny replaced Aug 2002
2. On the way home from tranny shop "Rough shift encountered followed by SES Light illumination". Returned to tranny shop, SES Light went out. Diags run - no problem revealed. Left vehicle with shop - unable to recreate problem.
3. Picked up vehicle. Drove home. Next morning "Rough shift encountered followed by SES Light illumination".
4. Took vehicle to mechanic. Diags run. No problem revealed. Reset Error Code. Mechanic commented that the gas cap may be the issue, ie make sure it is tightened.
5. Driving home "Rough shift encountered followed by SES Light illumination".
6. Took vehicle to Dealer. Diags run. No problem revealed. Reset Error Code.
7. Driving home "Rough shift encountered followed by SES Light illumination".
Does this ring a bell with anyone?

Sorry I don't have an answer for you on your problem, but I do have questions as to how you came about having to replace the tranny on your 2000 i.e. how many miles did you have on the original, what happened that you needed a tranny replacement, etc.?
I have a 2000 SE, myself. I'd like to know for future reference what happened to your tranny, just in case something happens to act up on my car....

Here'* alist of TSB'* that may help:

For the SC'd version go here:
http://www.alldata.com/TSB/48/004816FD.html

For the NA version go here:
http://www.alldata.com/TSB/48/004816IB.html

Let me know if any of these stand out to you & I can try to get a copy posted of it.

I'm not too familiar with the series 2 engines but this sounds like a problem that I had with my 94 ssei. The ses light came on shortly after i noticed the tranny shifting heavy and the rpms sitting rather high. It ended up being a vacuum leak. One of the rubber hoses came unplugged because it was real loose and worn out. All I had to do was buy a new hose for about $3. The location of the vacuum leak was under the cover right in fron of the supercharger. Check your bonne for any vacuum leaks