Woah.. alright, I'm done screwing this with myself till someone helps
Extracted the Deodexed_Stock.zip and put the 'app' and 'framework' (the two and only folders needed to be muddled around with to deodex a rom i believe?)
and put the files onto my sd card.
Tried to use root explorer to overwrite all things in /system/app from the deodexed rom.. it hit an error, went into a boot loop. Luckily I was able to recover using CWM.
Perhaps using pushing the files in ADB wouldn't of caused such a mishap?
Or, another idea, could I just simply take the boot.img from one of my clockworkmod recovery folders (i am on stock odex rooted)... and replace it with the boot.img in the original 'Deodexed_Stock.zip' file?
That would be me trying to fix the original problem of just trying to flash it and getting the boot.img error
I'm afraid to do any tests and don't have enough knowledge on ADB or the infrastructure to know if something is possible or if I'll cause another boot loop that I may or may not be able to restore (having CWM problems too)
Someone please help before I attempt any more experiments with this resulting in a deadened permanent brick