Fair enough, I figured the down and dirty way was to use my hex editor to create a BIN file of just the lower 512 of my 1024 dump. The only area with real data.   Make changes to that, run that through the checker tool and then put that back into the original 1024 byte BIN.     My understanding from reading is that in a 512 byte file, there's 32 addresses(?) each with 16 bytes.  the first 14 bytes are data and the last two are the checksum.   At work if I read or flash a file to an IC, there's a single checksum for the entire contents of the chip.  Is this so with what I'm working with and is the ECM also checking that?  If I modify just the lower 512 and leave the upper 512 alone, the checksum for the entire file will have changed.  Whether that's relevant or checked by the system I don't know.

As I said I would eventually like to put a 512 byte chip on my ECM but for the time being I want to leave the 1024 byte chip in place.  I don't know why they used it and don't want to create a problem for myself.  I assume it was because the 512 went obsolete or they had trouble getting it.  But, blank or not, in case the ECM is looking to verify the upper 512 I want to leave it in place.   Unless someone can confirm that part of the memory is ignored.

OK thank you for this info.  I was able to copy the lower 512 of my EEPROM dump into its own .bin file, make VIN/SKC/IMMO ID/Cluster ID changes to that file, run through checksum corrector and verify the data changed via the 95040tool --status output.   I copied the lower 512 back into my 1024 BIN and flashed it to the ECM.  It will still be nothing short of a miracle if it works but i'm hopeful. 
  I still can't find any info on changing the soft coding of the ECM from a auto to a manual.   The 4.2L Allroad was never offered as a manual so I'm still slogging through that challenge.  I know that on the 2.7T, you change the software coding from 07755 to 07715 (where 5=auto and 1=manual) but when I try and change my 4.2L/Auto ECM softcoding in the same manner, it reports an "out of range" error.  Stock software coding is 0007755.  I tried coding it to 0007715 with VCDS and it returned the "out of range" error. (I logged in with the SKC)
   Someone passed this post to me and I emailed the two gentlemen (PRJ and DDillenger) who claim they've handled this before......

http://nefariousmotorsports.com/forum/index.php?topic=3636.0title=

No Problem, thanks for the help. I'm much closer than I've ever been.  Hoping to hear back from one of those guys.  Or I may need to flash the ECM (main flash/tune) with a file from a car that offered both an Auto and Manual.  EG a B6S4.  That car has the same exact motor as the 4.2L Allroad but because it was an S4 they also offered a 6MT.  I have a ECM from that exact car coming in the mail (EBAY) so I can examine the soft coding.  Also maybe read the main flash off of it and copy it to my Allroad ECM.  Or leave the EBAY ECM as-is and update the VIN/SKC/IMMO/CLUSTER info. I'll have several options to try when I pull the trigger on this swap which should be in the next couple weeks.....

Very sorry to hear that. I guess none of us are guaranteed a tomorrow.
I do hope to hear back from PRJ , I sent him a PM. Thanks for the suggestion of Nubcake.  I will send him something as well.    It was my fear that soft coding wouldn’t work for the reason you stated.  And my best guess at the soft coding got rejected by the ECM (out of range!) so likely that confirms it. I have higher hopes that I can grab the factory baseline/flash off my B6S4 ECM and use that. Chomping at the bit for that to arrive.  Or just use that ECM period. (after matching the SKC/VIN/IMMO/Cluster info)  We shall see.  I still have my fall-back plan of contacting JHM.