Being somewhat new to this, I thought some notes might help others, and more experienced tuners may have some thoughts to add as well. The stock and modified files are below, and supersede what I added to the repository back when it was active.
The tune has evolved over time, including adjustments at different altitudes and ambient temperatures. Here's the notes, last modified in July 2023:
3.8L 2008JKR Wrangler Manual Trans
General Purpose Off-Road Crawl Tune
- Low RPM: Better low RPM idle-crawling from a combination of various Airflow, Idle Torque Spark & Throttle PID as well as Spark table changes bring out the low end torque smoother. It's also better when letting out the clutch with little to no throttle pedal.
- Spark: The Spark tables have changes to minimize spark knock and KR (Knock Retard) in less than perfect conditions like normal carbon buildup, hot weather, and heat soak at high load/slow speeds (sand dunes for example). Regular 87 (85 at higher altitude) octane is typically underwhelming, and the stock spark tables are optimistic -- at least on this engine. For example, at 1696 RPM the stock PT (Part Throttle) spark table is actually 3 degrees higher at 100 kpa than the WOT (PE Spark) table! Less spark advance when enriched (open loop) at the same MAP/RPM is obviously backwards. It probably made sense under test conditions, but makes the engine prone to spark knock in real life conditions.
- Cooling Fans: The temperatures and hysteresis (deadband) are reduced. This is probably better for everything, except fan lifespan and the tiny power it takes to spin. The new "on" setting is about where the thermostat is full-open.
- Fuel Temperature Compensation: In stock form the fuel trims go progressively positive as underhood temperatures increase, which is particularly noticeable off-road in slow speed heat-soak conditions. Changes to the Fuel Temperature-Fuel Mass Multiplier table fixes this problem. Note that the ECT (Engine Coolant Temperature) multiplier tested good during a cold start and warm up with the hood open -- very little trim change. But closing the hood and letting underhood temperatures rise created a positive trim change. After experimenting, the final values in the Fuel Temperature-Fuel Mass multiplier table ended up being about the equivalent of the coefficient of expansion for E10 gasoline, roughly 0.001/Deg C -- Which makes sense if it's designed like I think. Experimenting showed that if the slope is increased too much, the trims will instead start going negative as the underhood temperature increases.
- Volumetric Efficiency: VE tables changed to minimize the fuel trim change from zero. Only a small number of changes were beyond 1.5% and the graphed tables look smoother.
- Stoich and PE (Power Enrich): Delay bypassed under certain conditions and PE is slightly richer. Stoichiometric is increased slightly richer for today's E10 pump gasoline with about 10% alcohol. Note that the extra cooling from additional PE enrichment appears to delay entering the cat over-temperature enrichment which takes lambda into the crazy rich .7 zone.
- Speed limiter is raised from 99 to 128 MPH. You never know when that might be necessary...
In the attachments, the OEM file is the stock tune.