04 king cat efi 1000 cpc tuning help

who here has experience with this setup, I see lots of talk about 1000 cpc engines but almost all of them are on carb sleds. I put a fuel pressure regulator in and a pure logic tuning box and am having trouble getting rid of a rich bog at around 4000-5500. Once I pump the throttle a ton of times and get it past this It rips like crazy. Also the cpc head does not have water outlet for the throttle bodies, does this make a big difference? I have never run twin pipes before and am wondering if they all have some sort of midrange problem? Also some people have told me that twin pipes need lots less fuel in the mid range than a single pipe does, if this is true then can someone explain why! Should the air box be gutted or does this screw up the air temp sensor?
sorry for so many questions!

ok, bumped up the fuel pressure 3 lbs to 46 and it seems to run fairly well,
my clutching setup is 72gr weights, yellow green titanium in primary, 47 helix and red white spring in secondary. I don't understand how it could be rich at 4-6000 with the fuel pressure low and then clean up and run better when the pressure goes higher? the answer to the egt question is that it was around 900 degrees when it would start to sputter