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Are these JDM VQs I see advertised by various importers direct drop-in or there are pitfalls I'm unaware of? They seem to be all from automatic cars. I assume apart from the flywheel and ECU the engine is identical to the manual one, but is it really?
There are differences between the 5AT and the 6MT for the 2005-2007 year cars, it's an almost completely different engine called the "rev-up". These rev-up engines are usually hard to find so it's likely you're just looking at getting a regular VQ35DE and those mostly just comes down to flywheel or flexplate, and and pilot bushing for the 6MT or a pilot bearing for the 5AT (basically it's just a plug that fills the hole on the back of the crank for the 5AT).
Keep all your existing accessories, fuel rails, injectors, coil packs, every sensor, headers, literally everything. All you want is the long block from the donor engine.
I strongly recommend replacing the valve covers since you're going to have the plenum off to replace the injectors. It's a pain to do it in the car so you might as well freshen up the donor.
Also, replace the water pump and timing chain tensioner with new ones.
Verify exactly which engine you need, there are visible differences of the intake cam advance and exhaust cam magnet retarder on the two engines. The rev-up has the "waffle print" and the regular DE has the smooth faced one.
Here's a picture, normal DE on the left, rev-up DE waffle print and the blue/green harnesses for the exhaust retarders on the right.