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Cat Daddy,
Assuming that nothing else has been touched except the gear ratio, your ECM's may need re programming. What happens when you change ratios is that fuel, spark and air demands are all different than they were previously programmed for. The lower the ratio, the more load on the engine.
I experienced somewhat what you did when I went from 1.50 to 1.35 ratio, except my stalling occurred at 3,000 RPM. Once thru that it was fine all the way to WOT. Dustin reprogrammed the ECM's and she runs fun now (albeit a little rich at idle and we're working on that).
Changing ratios is akin to driving a stick shift car and setting it up for running based on shifting from 1rst thru whatever high gear would be, say 6th.. With the outdrive ratio change, now you're starting out in "3rd. gear and at 2,600 you're shifting to 6th. gear" and the ECM's going nuts.
Just for yucks, check to see that the manifold pressure line from the plenum to the MAP sensor is still attached at both ends. It fits over a barb about 1/2 way back on the plenum down low.
As to blowing out seals, we just removed our blowers after about 80 hours use (putting on the new engines) and of the three engines, one of them had the seals blown out at the plenum level, not where the blower attaches above the chiller. Even though they were gone, the black sealant Whipple uses was still there and we didn't notice any difference in the operation of the engine.
When we reinstalled the blowers, we used the sealant that Mercury uses on their outboard powerheads AND the rubber seals just to be certain.
We'll be dynoing the new engines at Chief this Tuesday and Wednesday and will be happy to provide any numbers from those runs to any Whipples users. The only difference between the new engines and the regular 500 EFI, is the new ones have Merlin heads with 310 cc intake runners and Crane Roller lifters instead of the GM's that come std. on the 500 EFI.
Good luck, and call if you have any questions.
Steve
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