Cheers dude,
I'm running a Silvertop 20 valve engines bottom end with a 16 valve bigport head and efi setup at the moment, 2inch straight through exhaust and new air filter... Heaps more but is easier for both of us ir you read some more of the thread, theres a bit in there!
As for your question, post it up in the mechanical section and se what people think. Sounds like its ignition related as its missing when started and breaking down under load... do the usual and check/replace plugs, leads, dizzy cap and rotor button. if there fine then start checking some of your sensors? Like I said, ask in the tech section and you will get alot of help, just be nice and give all the info you have!
Jarrad