built 302 runs like crap

I got an 87 mustang stock bottom end with stock roller cam, edelbrock performer intake, holley 670 carb, msd ignition, msd coil, long runner headers. The problem is the motor ran fine before i did all this work, then about 2 hours of driving it devolped a slight miss and then when i get it to 2500 rpms it starts misfireing actually feels like the motor is fighting itself, not just a misfire but like it fires before it gets to the top of the compression stroke. I adjusted the timing advanced and retarded it but with no resolve. I did put a new timing chain on and 99.9% sure the cam is correctly timed. Well i took the heads off and got a valve job done, resetted valves and .010 shaved off, put the heads back on and it ran great for about 4 hours and then it started to act the same way. I am at a lost, what the heck is wrong with my motor.

do you have a vacuum advanced distributor?

yes and i messed with the timing with the vacuum advance on and off

If the timing advance diaphram has a leak in it it will cause this problem.