the coyote continues to bite... resolved! :)

[toadster]

Having a bugger of a time with my Coyote Gen 3 crate engine (M-6007-M50C) with the Ford Performance M-6017-M50B Control Pack in my Factory Five Cobra

Lund Tuning and Ford Performance are stumped on this one, been trying to get this running properly since April

Setup is as follows - using VCM BETA Suite

• Gen3 Coyote Crate engine wired as suggested by Factory Five (everyone with a Gen3 coyote uses this guide)
• FPR set to 65PSI with fuel pressure regulator, and verified in VCM Suite
• removed the IMRC controls on the back of the engine, locked them open with MMR lockout kit
• engine fired on first try so all electricals seem to be good
• flashed with Lund Base Tune that accounts for my build, e.g. MAF/intake, removed IMRC, and I have catalytic converters in my headers
• the passenger side (bank1) runs great, gets up to 380F pretty quickly, bank2 (driver side) gets up to about 95F and backfires
• on initial startup it seems that bank 2 fires for a rotation or two, then shuts down that bank

from Lund: its being wonky from the start. bank 1 trends richer and richer then it cycles out of cold start emissions reduction and bank 2 AFR fails goes max lean and trims on bank 2 go to 97% lean correction.
its like that side of the engine stops firing. so far off that it eventually matches the correction on the bank but AFR still pegged lean. this is really weird this is the first I've seen this.

permanent codes - I'm told they'll go away after some drive time
P0356 - Ignition Coil F Primary/Secondary Circuit (Permanent) - e.g. cylinder #6 coilpack issue
P0124 - Throttle/Pedal Position Sensor A Intermittent (Permanent) - not uncommon on these engines I've been told and should go away
P2017 - Intake Manifold Runner Position Sensor/Switch Circuit High Bank 1 (Permanent)
P2022 - Intake Manifold Runner Position Sensor/Switch Circuit High Bank 2 (Permanent)
P2008 - Intake Manifold Runner Control Circuit/Open Bank 1 (Permanent)

troubleshooting:

• have swapped O2 sensors side to side, problem stays on bank2
• got a new 175T harness from Ford - no difference in O2 readings
• swapped coil packs side to side, problem stayed on #6
• swapped plugs from #6 to others - stayed on #6
• NOID light, all COPs firing
• tested all (4) VTC solenoids (2 bank1, 2 bank2) and all function with 12v tests (clicking)
• 3 pages of testing from Ford determined something wrong with engine harness, new harness shipped last week, seemed to get bank #2 up to much hotter (untouchable) temps but on next startup back to cold bank #2 running/shutdown
• checked all plugs, swapped out with new ones too - same issue

tl/dr; coyote fires up fine, shuts down bank#2 and doesn't come up to temp

seriously perplexed as to why this is happening, Lund and Ford are stumped as well... HPL file attached if anyone wants to take a peek at an idea...
hpl file: https://drive.google.com/file/d/1ZBl...usp=share_link
in order to use the HPL file, you can use the HP Tuners VCM BETA Suite