I bought my 2000 Q45 a couple of months ago. It had a rough idle (sometimes) with the Trac and Slip lights lit up. When this was happening, it ran very poorly at speed. I read many threads after searching and they usually went around and around regarding vacuum leaks and other external plumbing issues. I finally broke down and bought new plugs (the NGKs recommended in the owner's manual) and Hitachi coils and installed one side last weekend (the intake side, which is supposed to be more difficult).
After driving it for three days, I am very happy to report that it is healed. It runs great and very smooth idle. I am sure it was the coils, because the plugs had been changed a few years ago and were in good condition. Now I can do the "easy" side to finish the job, although it doesn't look like it is going to be easy getting that cover out of the way.
So, to make a short story even longer, I know the OP tried using a new coil to try to find the issue, but maybe a new set of coils will fix it. I know you hate to throw money at it. You can have my 4 known good coils if you want them (after I take them out).