Hard to imagine getting all the way to 7k on 10 degrees timing. Once your timing is advancing , you better hang on to your hat !

The misfire is puzzling... I might suggest wiring the fuel injectors in banks, setting to alternating instead of simultaneous and increasing to 2 squirts per cycle. This is referred to as semi-sequential. The misfire will cause the wild air to fuel swings. I suspect it may be flooding out and rich misfiring. A rich misfire will appear as lean... The warmup appears to be active even with higher engine temps. I haven't had enough time to look in that setting to confirm.

The idle VE table is enabled. This means you can tune down the lower rpm portions of the regular ve1 map... Perhaps lower the required fuel number. Wish I were local. Tune the idle table separately. Hard to say for sure not seeing/listening/smelling but this should help.

Warmup should be done around 160 degrees depending on your reference point.

Keep in mind that the temp measurement is being taken by the cylinder head temp sensor, NOT oil temp.
Once the engine is running, this sensor heats up real quick - well ahead of oil temp.

Yep, warmup is very, very short. Engine doesn't care what the oil temp is, combustion chamber temps are all that matters.

Any luck with logs with those few changes? I think you're way too rich/fat which could be because the required fuel value in the basic settings is too high or the VE1 table is far too rich in many cells. It could also be firing order/plug wires... a stuck fuel injector etc.

Made some reasonable progress tonight.
Ignition timing is now running on the ignition table. :)
Lowered idle VE settings significantly. Idle is now low and smooth.
Manually tuned out violent surging and misfire in the zone around 3500rpm/50% by increasing fuel in that area.
Killed off serious exhaust popping by dropping VE to zero along the bottom of the table. Not sure if this is the best way to deal with it, but it worked.
Did some tuning with VEAL.
Ran some logs, one attached at MS forum.
Smoothed out the VE table after VEAL roughed it up a bit.
Current MSQ also on MS forum.

Comments welcome.
VE table looks like this now and driveability is significantly improved. We are getting there. :)

http://forums.pelicanparts.com/uploa...1406127790.jpg

http://forums.pelicanparts.com/uploa...1406127815.jpg

Your post popped up while I was pulling my post together, but yes, I have had some progress.
Still getting my head around some aspects of the tune, but the engine is running much smoother mid-range after I made it richer. AFRs seem to have settled down a bit as well.
I am fairly confident that firing order and injectors are OK as we are getting good response now to tuning adjustments.

After a week on the sidelines, I managed to do some playing today.
Made some significant changes to the ignition table based on a map from another 3.6 engine.
Driveability is still quite good. Power seems pretty good ... not quite turbo territory, but real instant kick in the butt and good torque through the range as well. Waaaaay more than the 3.2 that it replaced.
It is far too easy to hit 7000rpm so I may need to turn down the limiter a bit.
AFRs seem to have settled a bit and I am now seeing 14's in large parts of the range, although it does go pig rich occasionally, so I still need to tune that out.

Starting is not as smooth as I would like, so I need to figure that out.
The IACV wiring has me confused. When ECU is off and IACV is disconnected, there is no connection between any of the four terminals at the harness connector or ground. When the ECU is powered, all four connector terminals are shorted to ground. I am chasing a resolution to this on the MS forum.
Latest tune file is also there ... here!

Good to hear that you got it running. I havent got any motivation to fine tune my ms ecu. I have only used yhe motronic... Maybe next summer. Last time i drive with the ma i had also sync problems with high revs. I have to learn from your progress.