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Fuel injection systems can be frought with their own problems. To compensate for high performance camshafts they need to be tuner friendly which some of them are not.
The same problem you have can transfer over to the FI systems such as lower vacuum from rowdy camshafts. This is where tuneability comes in and that usually means finding a good tuner with a dyno. That translates into a lot of money and $$$$. Re-education in your "system" would also be helpfull.
It can be done, but it can be frustrating. Just be prepared to spend the time and money.
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