Take a close look at the plugs when you pull them to make sure you didn't crack one while putting it in, or while messing with the headers. A bad coil is another possibility. I've had it happen twice to me, where the engine would start to crap out as it warmed up, because the coil was overheating.

 

The coil is fine. I just swapped it out with a buddy of mine. The box seems fine too though I will change it back to my old one tomorrow to make sure. I am going to change the plugs as well since they don't cost too much. Only other ideas that we have are either the pick up could on the distributor or the timing chain may have gone bad and jumped and is throwing off my timing...

 

You have a 3 month old engine. The chain wouldn't have slop like that, not unless the builder used an old bicycle chain! One other thing to check would be your valve lash. While the plugs are out, you might want to pop off the valve covers, turn the engine over, and first inspect the motion of the valves to make sure they are all going up and down the same amount. You're checking for a flattened out cam lobe, it can happen. Also check for rockers that are sloppy. The last thing is, it's possible the valve lash was initially adjusted right on the edge of being too tight, and now that things have worn in, they could now be too tight.

 

So I apologize for leaving that out but we checked valves and they all are okay. When we put tje rockers on we tightened them one turn instead of the standard half to three quarters. We did that because my buddy just had his built and they backed off after a while. We have the same rocker arms.
I see that the pick up for my distributor is only $25 so I'm going to pick one up Saturday and try it.

 

Any other info you're holding out on?
You adjusted the valves that way, after you started hunting for your engine problem, or before you had problems? And what procedure did you follow?

 

No the lash was set when we built the motor.

 

The further this goes, the more it sounds like a valve adjustment to me. I would definitely check them again, especially if you followed the two-step method that repair manuals give.
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