Try putting a ballast resister back inline before the coil....sounds like you might be overheating the coil (a very cheap fix if this is the case).
I got a truck a few years back REALLY cheap because the owner could not get the truck to run for more than about 15 minutes...truck dies...can't restart until hours later. The owner had removed the ballast resister and put in an aftermarket coil. Well, I got the "broken" truck, and with the ballast resister back in place the truck is fine, runs great, no problems staying running at all....I felt kinda bad for the guy, getting rid of the truck over a 5 dollar part. :oops: