I couple things some people are either not aware of or have overlooked.
You EEC is the main reason why it behaves poorly once warmed up.
At WOT, the EEC will pull 4 degrees of timing out once the Air Intake Temp gets to 150 degrees. At 135 degrees it'll pull 2 degrees out. I've seen some stock EEC files with this value as high as 8 degrees if Air Charge gets to 180 degrees.
Also at WOT, when coolant temp gets around 220 degrees, it'll pull 2 degrees out and at 230 degrees it'll pull 4 degrees. Conversely, when the cars cold and coolant temp is around 100 degrees or less, it will ADD 2 or 4 degrees to the timing.
So... when cold... it's up to +4 degrees on timing and when it's hot, it could be as much as -8 degrees on timing. Stock tunes generally only run 25-27 degrees max. So cold would be 30 or so, hot would be 13-15. That 12 degree swing is HUGE in how it performs.
Considering the stock tune turns the low speed fan on at 220 degrees and the high speed fan on at 228 degrees, there really isn't anyway to avoid this happening unless you have a chip or tune of some kind. The air charge decrease by an intercooler modification will avoid the 2-4 degree hit from that, but won't do a thing for the coolant temp.
That said, get a better IC, a 180 thermostat and a tune that turns that fan(s) on at 190-195 degrees and it'll be significantly better.
Good luck,
Steve