Since you just had to dive into it, there's a good chance it's something there causing your problems and not both coils going bad at the same time, as you already suspect to be unlikely. I know you've checked a lot of the little things, but make sure to take it slow and cover all the easy stuff before getting in too deep on the hard stuff. Battery terminals, connectors, etc. Edit: Something else I've noticed getting more and more mention here is the pick-up coil air gap(this falls into the after checking all the easy stuff category). Manual calls for .8 to 1.2mm gap. but when the gap is towards the bigger spec it's causing some people grief. If you get to that point, dial that in at the .8mm spec.
Haynes manual has treated me well so far. Haven't had to do too much diagnostic stuff beyond some charging system problems. Most my electrical and wrenching escapades have been on a voluntary basis. According to Haynes the primary resistance should be ~6 ohms, secondary ~15 K-Ohms, and spark plug cap resistance ~5 K-ohms, all measured at 20 degrees C.
Your TPS should not cause any drastic problems, but here's a link on how to check that widget.
TPS Adjustment. I could not get mine to match their numbers, but it was generally in the same ball park(blue/yellow=higher closed/lower WOT, and black yellow=lower closed/higher WOT)
Good luck and let us know what the culprit turns out to be.