I did a BHW into my XJ, which is somewhat similar to the same swap for a TJ.
Wiring: The BHW harness is insanely simple to 'thin out' in it's factory form, as it's built for a longitudinal engine bay. I'd highly recommend that you do your own harness given how simple the BHW harness really is. I eliminated the oil idiot switch, wired the alternator lamp wire into a switched circuit, and replaced the stupid vw dual coolant temperature sensor with a generic Bosch part that isn't as prone to failure. There's not much else to the VW harness. All that's left is a brake light normally open and normally closed switch signal, accelerator petal, vehicle speed signal, and clutch switch that someone else's harness isn't gonna give you anyway. Unlike the BEW/BRM there's no extra transmission wiring or anything like that, so it's really truely a standalone harness in OEM form.
Engine adapter/motor mounts: Randy of TDConversions is the man! He makes a remarkable adapter and his mounts kit is super straight forward too.
Flywheel/clutch: centerforce makes a 60lb flywheel. It's worth it's weight in gold, really smooths things out and gives you that slight additional mass to prevent stalling. A factory LuK clutch kit is more than adequate. People push huge ls power through the factory clutch without issue, so most TDI's will be fine.
Intercooling: I used frozen boost and put together an air-water setup. I've had some issues with mine, all due to mistakes I've made not their product. I'd recommend them in a heartbeat too. I used the factory intake manifold and 90° transition at the ASV for quite a while, been more than happy with that, but if you aren't going to run an ASV, I really like mecevo's race pipe. My ASV was sticking, and for less than the cost of a used one I just ran a race pipe. Since it's a manual I can stop a runaway by just using the clutch.
Accessories: I used about half of a BEW accessory mount and accessory pully. I chopped power steering mount off for frame interference, and relocated the pump to the factory ac compressor location, but maybe you won't have the same clearance issues. I put a off the shelf sanden sd7hd ac compressor on the other side of the block like a BHW would have, but only used one belt with the BEW tensioner. If I hadn't also put a York air compressor directly above the alternator, it would be perfect.
What would I change with this formula on my Jeep? Better intercooler coolant line routing, run the air compressor off the same serpentine belt as everything else. That's about it. It's a wonderful setup, and how things should have been from Toledo in 1998 when my Jeep was built. I've put over 10k on this thing since October, and it's a dream to drive.
I've documented my build fairly well if your interested, since the TJ and XJ actually have quite alot in common, and I'd happily answer any other questions if you have any. I included a very good wiring diagram in one of my posts in my build thread that is much easier to read than the factory BHW diagram if you decide to go that route.
At the end of the day, the coty stuff is nice cause it's a "kit" but if you've done one swap (you've done many from the sounds of it) you should be more than equipt to roll your own setup.
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