ohhh lordy how i hate the zephyr boards XD
well for 1 thing lets tackle one thing at a time here:
have you tried simply using the download clean NAND button in JTAG tool and injecting your KV info, as well as un-wireing th JTAG points just to see if it works as a retail 360?
from what i have gathered from what little bit of modding i have done 1 mod at a time, it sounds to me like your trying it all at once just do one step at a time to help eliminate issues
for example build stock NAND from donor KV and what ever else you need to do and ensure the system works as it should as a retail, if it works properly and you successfully rebuilt your NAND than move on to re-wiring your JTAG points and move on to flash xell, and move down the flow chart as long as things keep working properly
once you run into your actual problem in the process it will than give you some where to start looking for problems be it human error or JTAG tool not functioning properly or what ever
this is just my suggestion Martin up there has been around a lot longer than i have but this is the process i would take in you scenario just to help narrow down what exactly the problem is
if it dosent work after building the retail NAND and trying to have it function as a normal 360 than either you are inputting the wrong data some where (like the CPU key) or JTAG tool is messing some thing up or some thing along those lines
but ya all in all that is how i would narrow down your problem hope you get it figured out i hate these zephyrs XD