First off I want to start by thanking everyone here for the abundance of information I have tried to sift through over the  past few years (though I have only been a registered member for a little over a week). Thanks to your efforts, I have been able to get as far as I have.

A little background... I purchased a used 2002 A4 5spd Quattro about 7 years ago. When I got it, it had some slight mods (ECU flash tune, diverter valve, VW CC 17" wheels) Since then I have added quite a few modifications (FMIC, coil packs, 034 high flow cat, Billy Boat stealth exhaust, ST coilovers, RA4 stg2 clutch conversion kit, s4 rear sway bar, DW200 fuel pump, Fluidampr balancer, Hex-V2 VCDS) and I am finally at a point where I would like to install a low mile K04-15 that a friend gave me when he upgraded his car. I have heard that this can be run on a K03 tune but was looking into tuning the car myself (never tuned an Audi but have previously tuned some personally owned Chevrolet and Honda ECU's. I am an electrical engineer by trade and would consider my self decent at programming both PC computer software and micro controllers. With that said I was hoping I could get some advice and/or assistance on my current issue. I would like to keep my current ECU intact with the ability to run the car, and I would like to code a backup ECU to eventually replace the current ECU for daily use once I believe the ECU is tuned well enough.

Question #1 - ECU Compatibility
The ECU currently running the car has 8E0909518F ME7.5 0001 on it. I was able to purchase an ECU from local junkyard that has 8E0909518F ME7.5 0003 on it, and unfortunately didn't notice the difference until i was at a point where I couldn't return it. Am I ok trying to use the new ECU or do I need to purchase one that has the 0001?

Question #2 - VAG cable for ME7_EEPROM program
In a search for information to clone the existing 95040 to the new ECU I found that I couldn't use my Hex-V2 in passthrough mode so I purchased a Vag-K+Can cable off amazon with the hopes of using it with the ME7_EEPROM tool. I was unable to read through OBD always resulting in errors so I borrowed a friends "Blue" KKL VAG-Com cable which resulted in the same errors. Both cables seemed to have FTDI drivers loaded with no issue on Window 10, Do these cables need specific drivers to work with the program?

Question #3 - 95040 Page information
After reading a bit more I found that even if I was able to read it, the EEPROM dump would be incomplete and missing some of the data needed to get the new ECU working on the car. However I was able to determine that some hardware I already had was capable of reading the 95040 chip in the back of the ECU using a SOIC 8 test clip (keep in mind I was trying not to remove the chip from the ECU to reduce the possibility of being down a car do to any issues like pad lifting). I was able to read the current ECU and the new to me backup ECU with this tool, saved both dumps to my computer and tried writing the dump from my current ECU to the new one. The results did not start the car.

Upon further investigation and re-reading the current 95040 several times I realized that between reads data seemed to change in page 0x00000110, which is the one right below the page containing the what I believe is the IMMO-ID. In all dumps the VIN, IMMO-ID, SKC, Engine HW code (8E0909018), and Engine SW code (8E0909518F) all seemed correct. I was thinking this could be caused from a bad connection to the chip with the test clip but it seems odd that data before and after this point are consistent. Is there data stored on this page that is important to the ECU's ability to start the car?

Question #4 - Can SKC between ECU and Cluster be different?
One thing I did notice when combing through the current ECU dumps was that the IMMO bits in 0x12 and 0x22 were set to disabled by who I can only assume was the company that previously flashed the ECU it with a tune, Unfortunately I do not know what company the tune comes from and was only told that it was flashed with a stage 2 tune when I purchased the car. My first thought was to flash the new ECU with a virgin file and perform the adaptation through VCDS but I believe the SKC pulled from the current ECU does not match the SKC for the cluster. When I tried to login to the ECU with the VCDS using the SKC retrieved from from the ECU dump ("0"+ bits 0x33,0x32) it didn't prompt me with a pin error, however when I tried to login to the cluster with the same pin I got a prompt saying the pin was incorrect (I only tried this once). When looking in VCDS, the Engine -> Adaptation has "Malfunction" in the first field, and the Instruments -> Adaptation has "Disabled" in the first field. Can the SKC be different if the IMMO is disabled and still run the car? Secondly, if the SKC is different will the adaptation process even work?

I apologize for the length of this post and would like to express my gratitude in advanced for any help. Please let me know if there is additional information i can provide to aid in the debug process. Please also try to understand I am a bit hesitant to post my raw bin dumps on the internet containing sensitive information about the car.

Thank you Marty for the clarification.

Any Thoughts on the page information that seemed to be changing when I would read the 95040 chip in circuit and why it prevented the car from starting? From all the info I have gathered, that page has no relevant information or checksum. Also, am I correct in saying the ME7_EEPROM tool from ArgDub is not going to read all the information I need to flash the new ECU and using a standard EEPROM reader is going to be the best method for this situation?