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Stainless & aluminum is a bad mix, some alloys worse than others. Use anti-seize if you want them to be removable in the future. If the nuts are stainless you'll potentially have even bigger issues, again depending on the alloy; some stainless types will gall and stick badly.
Changing engine and/or transmission types can lead to electronic control issues so I'd suggest keeping it all the same unless you know what you're doing. I'm good with mechanical and afraid of electronics/programming, but to some that part is easy.
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