I've taco'ed a throttle plate with the M62 on mine, it was not fun.
Suck through throttles or dual throttles-blow through throttle with a PD supercharger with no bypass valve is dangers. Regardless, you MUST MUST MUST use a compressor bypass valve with any Eaton blower! Not bypassing the blower at idle and low load will result in the blower overheating and seizing solid. Leave the blower unbypassed at idle for five minutes-it'll lock up solid from the heat. Never mind the stop-and-go of traffic...that'll lock it up even faster!
I have two seperate throttle cables operating two throttle bodies-a 60mm on the intake plenum, and an 88mm on the inlet of the supercharger. I modified the inlet of the M90 case to allow the full 88mm throttle. The quadrant arms are different sizes on the two throttle bodies, so I had to make matching quadrant arms to make sure the two throttles opened at the same rate as I pushed the throttle pedal.
You should be able to mount the blower anywhere you want-but the merc blowers are not what you want to base your design on. That clutched pulley wears out and won't engage, and if you're like 99% of all the people who want to use it specifically for that, I've got news for ya-no mad max style blower engagements. It'll immediately burn up the clutch and will never work properly again after that. The blower is normally held engaged by the computer, and the computer DISENGAGES it over a few thousand RPM-it's only working for idle-3000-3500RPM and then the computer drops it out and bypasses it. Also, it's very expensive to get an interchangable or any other size pulley for the blower...500$ plus last I checked into it. No other systems will fit it directly.
Also, the blower doesn't have to align with the intake. You can cut and fab a new plenum to mount the blower, and put it anywhere you please to get the belt lined up, from what I remember the intake side of a quad-4 has lots of room under the intake manifold.
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