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Fun project! Scott is a friend of mine and he has done a bunch of 996/986 conversions now. The chassis is talking to the motor just fine on them so you should have no problem with that. Toyota 12v PS and WP are the only way to go. The LS3 is certainly a tight fit but doable and it is a sweet powerplant with monstrous torque.

You may be able to use a Cayman engine cover to fit over your intake. It is a little taller and some have done this successfully. Forget a plexi cover. The way a Boxster breathes by pulling air up from the road surface makes the engine compartment look like a nasty chicken coop after about a week of driving. It ain't pretty and this is actually part of the ground effect in addition to cooling the accessories, trans and rear brakes.

I have considered this conversion but Nazi emissions regs in Comiefornia make a street conversion risky. I would have to register the car at Scott's house in NV and run the CHP impound gauntlet while living here in CA. Too much PITA for me unless it was a dedicated track car.