For the brightness, i don't know why it's doing that, haven't heard of that problem before.
For the Market, the update may or may not fix your issue, i've had to do that before on both themed and unthemed versions.
For the LauncherPro issue, I would try reinstalling it. Two ways to do this. If you have an update.zip patch lying around, open it up with 7zip (don't extract, just open), remove whatever it is in there that the update is for, like my Swype, remove Swype.apk from the system/app folder. Open up my theme zip, then copy the Launcherpro.apk out of the system/app there an drop it into the system/app folder of the now blank update.zip. Drop this onto your SD card and install through recovery.
Or you could install the ROM, then Theme over the top (IE without wiping), and then any metamorph changes/patches you installed. That way you don't have to replace all widgets, settings, stuff like that.
Or you could just do like you said toward the end and sbf then do a full install.