Totally forgot to update here.
Car has been back on the road for a while now, running normally I think. It's very slow but according to everything I have read a 11 sec or so 0-60 is normal lol! Feels good in 1st/2nd but needs more revs than I would think to not lug, doesn't really do anything past 3000 in terms of more thrust but it does feel very nice to drive overall vs other 4 cyl manual cars I've driven. Lots of pleasing noises and not too horrible at cruise.
Swap process went fine other than I was extremely lazy and didn't order timing tools until after I already had the new belt etc on the engine, I just did it by eye/scribe marks and somehow it was correct. I may have also had a bet going with someone that if you are careful enough with marking everything you can get away with it....worst case it would have been off enough that injection timing couldn't be adjusted in VCDS and I would have had to do it again with the tools.
All new suspension and steering, tires, axles, bushings, links, brakes including master, LUC clutch kit, all engine seals, filters etc etc.
Also had to fix all the random broken stuff, CCM was dead, drivers window reg had the usual snapped cable, center console latch was cracked, replaced the headlights and all bulbs, took the interior out and cleaned everything, replaced door seals and made sure trunk seal was good. Typical stuff on a 300k+ mile car that the last few owners just kept running into the ground. Last major thing I need to address is the headliner and front door card leather inserts and a new glow plug harness.
New engine works well, no worrying blow-by or compression differences. Did a carbon cleaning before installing and am running an EGR delete to try and keep it clean, full straight piped because it came that way and I honestly like the turbine noise. It's not nearly as loud as I feared/the engine itself is so damn noisy the exhaust almost doesn't matter.
MPG is great, I thought the fuel gauge was broken at first since I bought the car with 2/3s tank and after 30 miles it didn't notably move. I refilled it and it took the amount I expected and the gauge also moved to full, since then I have gotten used to it barely moving lol! Once all the who knows how old fuel was mixed down/several tanks gone through overall running stabilized and I have been getting about 55-65mpg depending on what I am doing.
If I can keep those numbers and gain perhaps 30? hp this would be a perfect daily with just enough power to not have me worried, the 5 speed makes the car IMO. I tried a few times to break 100mph and it's so painfully slow past 70 that the best I could do on a 2 mile backroad was 89, I would like just a little more than 1mph a second lol!
The project will also fully pay for itself in 27k miles vs driving the Jeep