Greetings Community, thanks in advance for giving this a skim and sharing some thoughts. I'm a bit stuck.

Background
I'd rebuilt E30 and E36 cars repeatedly in the 90's and 2000's (and drove SCCA off and on), but bought my first diesel a little more than a year ago and sorta fell in love. It was a high mileage 2009 X5 35d, but like many others have commented, the torque and handling and overall utility of the thing caught me off guard. Love it.

Aside from minor updates and maintenance it was great for 9months of high-mileage driving (~3 to 4,000 miles a month), then my harmonic balancer went (so I added a Fluidampr main, and clutched alternator pulley from AARodriguez). Then a couple months later something popped and I lost all low-end acceleration. In doing rule-out with my local friendly indy shop, we figured it was most likely the small turbo, and since I was planning on doing emission deletes anyway, we decided to do it all at once.

The work
So we pulled the DPF, EGR and SCR/Cats (using the procedures in these forums), and replaced with ATM bypass pipes. Also put in a new OEM small turbo (and we discovered the original had shredded fan blades and a loose main bearing). Put everything back together and it ran...albeit, with codes. But we could clear them, drive gently with just a CEL as a result. (if we stomped on it the X5 would generally drop into limp mode until re-cleared).

The problem
So I pulled the ECU and shipped it away for re-mapping. The X5 didn't move for a week. ECU came back, plugged it in...and no start. Punch the start button: dash reads "pre-heating," then a ~3sec delay, then engine turns over but won't catch for ~2secs, then it cuts off.

Replaced the battery with a new one, just in case, checked that it was coded correctly (using Carly). Checked everything we could (connections, etc), found no issues. Coordinated with the tuning shop to remotely re-flash the ECU: ECU seemed to correctly communicate, accept the flash, and thereby confirm the ECU is okay. Still no start. Flashed with the original stored backup image. Still no start.

I'm getting these consistent codes out of Carly:

Engine / Motor
Fault Code: 004390
Fault Explanation: Charge air temperature sensor signal
Fault Code: 004794
Fault Explanation: Low pressure Abgasrueckfuehrsteller, control Fault Code: 004709
Fault Explanation: Reducing agent pressure sensor, signal
Fault Code: 003F01
Fault Explanation: Boost pressure sensor signal
Fault Code: 004000
Fault Explanation: Fuel temperature sensor signal
Fault Code: 0046F4
Fault Explanation: Reductant active tank temperature sensor signal Fault Code: 004207
Fault Explanation: Lambda probe heating control

I dont know that there's any connection between any of them, other than electrical anomaly.

I'm at a bit of a loss for how to proceed: part of the problem is that I live in an area with only 1 BMW dealer, and they have a 2+ week wait for service. There also aren't any "pure" BMW indy shops, and just a couple "Euro" shops like the guys I use. Nice guys, but not tons of experience or all of the right tools.

So my thinking is along these lines:
1. Something completely random and unconnected happened while the ECU was out of the car, and I need to forget everything else and find a way to troubleshoot.

2. The tuning shop didn't *really* re-flash with the original stored backup, so the problem is with a bad flash.

3. Something physical happened to the ECU in transit: for example, broken solder at the bus joints are letting the main silicon communicate with the diagnostic device (laptop), but preventing other sensor systems on the car from communicating with the ECU. So do the codes above suggest a bus connector is not connecting?

4. EWS/CAS: because it turns over, but sounds like either no fuel or fire are getting to the cylinder, it makes me think there may be something going on with the EWS or CAS system. But I confirm the key/EWS aren't generating any Carly error, and I gather it would crank longer in that case than just the 2secs before cutoff; and I understand also that this E70 iteration auto-syncs the CAS and there isn't a coding process to perform. So.

Could some of the smarter-than-me E70/35d folks chime in and give a thought? I'm at a bit of a loss for direction. (And the mech shop is saying "it worked before we took out the ECU," and the tuning shop is saying "the ECU tests out and communicates fine, so that's not the problem...")

Thanks much!
Drew