Hybrid wiring harness/Engine swap questions

I am looking at buying a newer engine for my 1991 Jetta Gl that just went. Most of them that I've found on VW Vortex are out of newer cars. I have really been looking at getting a 16v 2.0L out of a Passat or Golf. I know that the engines have different fuel systems. I was wondering what the best way to do this is. Run 2 harnesses in parallel (heavy and space issues) Cut and splice. (What and where do I cut and splice, are all of the motor controls handled under the hood?) Something else?

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Matt Anderson
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