Hi All, been lurking about and I'm stumped so I'm jumping in to my first post, sorry it's a long one:
The car: 2009 R56 Base Hatch 70K miles. Bought 6 months ago, wrecked with undercarriage damage. PO hit something low, no body damage, but hit the transmission pan and drove block back, cracking mounts and steering rack. Repaired and ran great for 6 months.
Me: Have rebuilt several E46 BMW's, but wife always wanted a Mini, so this is our first. Have done everything from tune ups to full motor swaps, and some experience with ISTA/INPA/NCS Expert on BMW's

So ... car was running great for first 6 months. In the last few weeks, started throwing engine light (MIL), and ISTA scan showed random intermittent BUS communication errors, but no 'mechanical' faults and no issues running and driving. With communication errors, ISTA shows some (random, changing, and intermittent) modules not communicating, but I can click into each module, and all functions on ISTA work, including component triggering for the functions of each module. Clicking 'test ecu' results in module showing as responding properly and the code then comes off the ISTA fault list.

With the car starting and running fine, I (of course) put off running down the bus communication errors.

Couple days ago the wife mentions that car is intermittently running rough and has stalled at stop signs. ISTA shows misfire cylinder 1 and some more bus errors. Clear the misfire code to see if it recurs because car is starting and running fine at the time.

Next day wife limps home with rough running and stalling and dying on acceleration. Same cylinder 1 misfire and more random bus errors (not the same modules as before). Managed to get the car into the driveway and now cranks but no start.

Com errors move around on all buses (pt-can, d-can, MOST) but modules are still active and responding to commands with ISTA when directly called up.

Check cylinder 1 coil/plug, looks ok, so went to switch it with cylinder 2 to check coil and found oil in cylinder 2 plug well ... pulled all coils and oil in both cylinder 2 and 3 plug wells. Pulled valve cover and found rock hard and crumbly valve cover gasket. Valve cover gasket/grommets replaced. Plugs didn't look overly fouled, but all were replaced. Valve cover gasket was not bad enough to leak to exterior, and no vacuum/pressure codes had been thrown.

Due to oil in plug wells, checked cylinder compression, all 4 ok and within 10% of each other. Have not done leak down test yet because compression looks good enough and engine was smooth until 2 days ago.
Checked spark, all 4 cylinders/coils sparking on inline tester.
Checked fuel pressure at the rail, 50-51 psi on cranking, which i believe is perfect.
Fuel pump primes on door open, and responds to ISTA component triggering by correctly coming on and running 20 seconds when commanded to.
Battery pulled and tested good, fully charged off the car, and replaced in car with a 13V constant power supply hooked up to it .. No CAN bus errors, no error codes (on ISTA scan), but still crank and no start.
Cam/Crank position sensors good.

Checked fuel injectors with ISTA component triggering function, and ISTA says (on all four injectors):

"Function: Fuel injector 1 off (only when engine running)
"State: Switch-off active (emissions warning light on ===> Delete fault memory"

ISTA shows no faults, but I hit clear faults anyway, and injector switches to running state ... crank no start, and upon cranking injectors instantly switch back to "Switch-off active (emissions warning light on ===> Delete fault memory."

At this point, seeing the fault memory status, my idiot brain finally looks up and realizes the dash MIL light is still on, even though i cleared faults through ISTA and ISTA itself shows no faults.
Trying to figure out why ISTA would show no faults when the dash light is on, but even ISTA apparently thinks there's an un-cleared emissions fault, i go to autozone and get their generic code reader. It also says no pending DTC codes, but the reader has a yellow LED on that the book says indicates "A pending DTC present and/or some of the vehicle's emission monitors have not run their diagnostic testing".

So, FINALLY getting to the point ...

1. What reasons would there be that ISTA and the autozone reader both show no DTC codes, but I have a MIL light on the dash and both ISTA and the autozone reader think there's an emissions error of some kind?
2. Does that ISTA status on the injectors mean what it says, that they're "switched-off" or does that only mean the engine is off at that moment that it's status is being checked?
3. My understanding is all bus communications pass through JBE, which appears dry and no corrosion, but what part of the JBE/Fuse box is the CAN communications coming through so I can try to clear up the electrical gremlins?
4. What do I try next?

I have INPA for my e46's, but don't have the daten files for the r56, does anyone know a trustworthy & reliable download source with install instructions because I've never had to update daten files before?

The wife has wanted a Mini since Gen1 first came out, and I got some serious brownie points for 6 months for hooking her up. Now she's looking at me kinda funny, and asking me 625 times a day if I've fixed her car yet.

Sorry the first post was so long ... go big or go home right?