What I did with mine (using a Big Block chevy/TH400) was to start at the transfer case, so to speak.
I first dealt with the positioning of the trans yoke to the transfer yoke and stub shaft length, along with modifying the trans crossmember for the GM mount, then put the engine where the intake was level and the side to side was even afterward. In my situation, I had no engine mounts on the frame and had to fab those myself, so I wasn't limited to placement there.
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