I don't know what exactly fixed it for sure. I just took the stock system.img from the complete non powered on nandroid backup posted, extracted all the files(using unyaffs.exe) and went through and auto deodexed framework and app using an auto deodexer tool found on xda, then the files taht wouldnt auto deodex using that .bat script, I used the baksmali and smali jar files to manually deodex the rest. I kept geting erros on the DbgCfgTools.apk(but ir ead up on the erros i was gettinmg and some of the htc sense roms were getting erros on some of there files like that and they said to use the -I option when baksmali'ing the odex file and it ignores the errors I guess, but that app was refering to bootclass paths that are no where in any .jar file on the phone so it's likely that apk didnt work in the first place cause if it was called to, it would display the same bootclass errors.
Yeah you can link to this, and I will make a stock deodexed rom that also formats and replaces everything in the /hidden partition(i.e. all the bloatware) as well as a bone stock rom so someone who has messed up the hidden partition can get back to bone stock easily!