The boot screen may appear to have lower contrast because your Xbox is now booting in NTSC mode, and NTSC has lower contrast than PAL. Don't worry, once it finishes booting and starts outputting real HD then it should be fine....
You only have Krayzie Extras if A: you installed it manually, or B: you used HeXEn to install / update your softmod. The standard Krayzie installer doesn't install Extras, because it's too large to fit in the gamesave.
I'm struggling to understand how you have HeXEn tools but not Krayzie Extras..... All I can presume is that you have used HeXEn to update your softmod at some point, and have then manually changed and deleted stuff (i.e. installing Avalaunch), then tried to use HeXEn tools.
You do know how to disable the virtual eeprom - you used eeprom_off.bin to do just that. You only need Krayzie Extras to update the virtual eeprom.
If you have updated the softmod with HeXEn, even if you have replaced the dash with Avalaunch then you can update the softmod by simply running UnleashX (E:\Dash\UnleashX\UnleashX.xbe), then go to Xbox Admin - HeXEn Tools, then select "Enable HD video modes" and follow the instructions.
Nothing you have described should have removed the backup dashboards from E:\Dash\, so if they are missing then you must have done something else that you forgot to describe... but I now realise that when you talk about Avalaunch you almost certainly mean UnleashX!
The question is, when you boot the Xbox normally, and run XBMC, what does it say the video mode is? Then, if you boot with HeXEn and use the File manager to run XBMC, what does it say the video mode is?
Try running HeXEn option 2.3.7 - Remove unwanted eeprom copies, then repeat, and see if the video looks any better, or if the video mode changes when running with a normal boot then with a HeXEn boot.
Enabling HD on your chipped Xbox is easier, because you don't have to worry about the virtual eeprom - you just run Enigmah, then run XBMC and change the settings
