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I'd take the motor and tranny out, then attach the tranny to the new motor, and lower them both in. It was easier taking all of the brackets before lowering it in too.
Pull the tranny with it, not sure that the 1 motor mount would hold the tranny and then you won't have to balance it and try to bolt it to the engine...would be a HUGE problem if you left it in.
Seriously.... I've got a d15b7(auto) ready to pull out of the 93DX and waiting to pick up the 95 EX d16z6 and swap em out. Both will get pulled with the tranny intact....Jack