Well, I decided to drop this thing at a shop, since I couldn't figure out the blinking light thing.
The nice gentlemen at Bavarian Motor Sports in Suwanee, GA put in a good show to get this thing running right again.
The MAF was fine, there were no codes, and no vacuum leaks. Turns out that the plugs I put in in March were out of range, and causing various problems with the coils. Now, I thought I had a slight transmission slip for a while (I hate
automatics), but it appears that was engine surging.
The car has the proper plugs (Bosch copper +2's) and new coils. It runs great and I'm hoping some of the other mysterios maladies are going from the electrical system.
This would be the pat of the post when I echo the sentiments of those no this board who tell you to varify that you are actually putting the correct parts in your car. All the plugs I ran were listed in the parts store computer as 'better than stock' or "OEM" but none were actually the factory/dealer recommened replacement.
In an effort to save $30.00, I ended up costing myself over $500, not to mention 8 months of stressing about a transmission rebuild. Luckily, there wasn't any collateral damage beyond the coils.