The coil shouldn't be breaking down when hot (or not to my knowledge).
It still sounds like you have a vacuum leak.
Triple check for vacuum leaks (including the vacuum tree behind the return plenum by the firewall). I'd mentioned in posts above, the vacuum leak that I had a couple of years ago was miniscule and hard to find. The car running and spraying water on the hoses yielded nothing....no dying out, no leaks, nothing. With the car not running, I sprayed the hoses and then connected some PVC hose to a connection on the back of the plenum and blew into it (there's more than enough pressure in a good set of lungs to find a leak), and sure enough, some bubbles had came out of one of the hoses on the intake plenum.
The reason why I'm still wondering if there's a small, almost undetectable vacuum leak is because my car didn't run well when it would start to heat up (ie: when the temp gauge would start to register movement). It would run great when starting it cold, and it would run pretty good when it was at full operating temps (though a little erratic in the idle). When trying to start the car up when it was hot, it would be more difficult to start, and would crank weird......like the battery was dying. This was pretty embarrassing, since the type of quick, in and out trips to places like 7-11 would result in the hesitant starts. Another crank or two would always get the car up and running. But it did feel like the timing was off, like what you are describing. And at stoplights during the periods when the engine would just start to heat up, I would have to have one foot on the brake, and the other on the accelerator and have to keep the idle RPM's up a little higher than they normally would be, otherwise the car would stall and die out. I kid you not!
I had replaced the hose clamp on the problematic hose/ connection.......the guy who had the car before me had tried to tighten it up when it had somehow formed an oval sort of shape instead of a round shape. It sealed up well enough--but not well enough under pressure. You may just want to buy new hose clamps at all the connections coming off of the intake plenum.......for a couple of bucks, you'll have the assurance that they're clamping well. Another thing that I've noticed is that the smaller hose clamps can get damaged pretty easily if they're torqued too much.....the grooves on the clamping part get distorted and bent and they may not really torque down too much.