Hey all, I'm new to the forum and just had a simple question, Is it possible to take the 3.6l and a 6-speed trans from a Jk and install it in my TJ? I don't want the "Just get a JK" answers either, I have too much of a sentimental value for my TJ. Really, what it comes down to is if it is possible. My gut says it will fit like a glove, but my conscious says otherwise. Any knowledge on this subject? thanks everyone!

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It is possible, and you'd likely be the first one!
If you're not too savvy with engine controls and wiring check out Novak and Advance Adapters websites. They've built some good conversion systems for gas-powered engines.
Think of your TJ...any TJ, as a "networked" vehicle, in respect to how the engine computer, ABS (if equipped), Air Bag, etc interact with one another. Now multiply that complexity by a factor of 10 and you have a JK. Each generation, YJ, TJ, JK, became greatly more complex than the previous, with the JK being a 100% systems supported network using a CAN backbone (think LAN Ethernet in a building). The 3.6 is about as advanced a powertrain that's on the market now, with variable cam phasing, timing, etc. Great stuff, and very efficient, but complex.
Good luck either way, and keep researching.