I had a very similar problem as well. I ended up doing an Opti swap. I got a replacement from Summit, put on my MSD Cap & Rotor, and ran new spark plugs & wire and the car ran like a champ!
I would check the spark plug wires first. I was running Taylor 8's and I think they were my problem. The car would run great for about 15-30 mintues, then it would start to brake up with anything over 2,500rpm's.
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