The deck height is about 19mm higher for the longer stroke, but all that means is you need 3.5 timing belt, and you'll have to figure out accessory belt lengths. There will be a problem with the exhaust length too, but if you use 3.5 mani's and downpipes, it should work. You will be increasing air flow, and I'd rather use the 3.5 ecu and harness if possible to get a better match in case the 3.0 maf doesn't have enough range.

Not responsible for advice not taken...