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What year engine and TJ?
What state inspection requirements?

These are big issues many places. Often the engine needs to be newer or equal in age, and factory type emissions present. A carbed 350 may be starting with 2 strikes against you.

You'll need to upgrade the d35
 

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The problem is I have no wiring harness that came with the engine. I used the engine for a derby motor so I never needed the wiring harness so got rid of it.

So what I need help with is, will not having the wiring harness kill me when swapping, what auto transmission should I install (been thinking about 4L60e and using the transfer case that comes with it), is doing the ford 8.8 rear axle swap difficult to do or is there an easier cheaper way or could I just change my gear ratio in my crappy 35 that I have now? Any guidance and help would be great. I have looked into this for a long time now looking at other threads and novak and still want to clear up as much as possible.
You want to retain the factory harness unless you want aftermarket gauges. Just read a thread where someone balled the whole factory harness against the firewall and left stock PCM in place. Added new harness, new computer, and used just a couple inputs needed for gauges on the old harness.

Is your 350 computer controlled? The "e" in 4l60e is for electric or computer controlled. If you have an old school 350, look at just a 4l60. Otherwise a 4l60 is a good small block trans.

8.8 is a good option but not a bolt in like a 44. The 44 probably not as cheap.
 

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Take a look at Hotwire owned by Tony Squier. He can answer all your wiring questions.

With no PCM, and if you want an electronic controlled trans, Powertrain Control Solutions makes programable transmission computers. It does add a layer of cost and complexity when a mechanical trans seems more at home with a carbed 350. Some trans mechanics still only work on non-electric transmissions....and typewriter repair used to be an occupation.
 

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Take a look at Hotwire owned by Tony Squier. He can answer all your wiring questions.

With no PCM, and if you want an electronic controlled trans, Powertrain Control Solutions makes programable transmission computers. It does add a layer of cost and complexity when a mechanical trans seems more at home with a carbed 350. Some trans mechanics still only work on non-electric transmissions....and typewriter repair used to be an occupation.
 
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