We definitely need more info on your combo.
Going just on what you said, I agree with BK_CAULEY. With a SC, you need to be sure you are giving it plenty of fuel. You need a high volume fuel pump (255lph), and either big injectors with a matching MAF (preferably with a custom tune), or if you are using stock injectors, you MUST have a FMU (fuel management unit). The stock injectors can't flow enough fuel with the stock fuel pressure. The FMU responds to a boost signal by progressively restricting the return fuel line as boost increases, increasing fuel pressure to the injectors, forcing more fuel through them than they are designed to flow.
When you say you unhooked the intake tube from the SC, do you mean you hooked the MAF (mass air flow sensor) directly to the intake, like on a stock setup, simply bypassing the supercharger? And when you did that, it works fine, and you can go wide-open past 3500 with no problems?
One other thing, it's possible you are blowing out the spark with the supercharger, if your plugs are gapped to large. You could gap them down smaller (maybe around .035) and see if it makes a difference. But FIRST, I would figure out if your fuel system is adequate. If you are running it lean with the supercharger, you run a good chance of blowing your head gaskets.
So before you do anything else, tell us about your fuel system...
Jeff