I'm almost 100% sure this happened due to the initialize_build_db step, if you comment out this line in Makefile.linux
@${RUN} ${SVNROOT} Init_Build_Database ${DB_USER} ${DB_PASSWORD}
It should build all the Ubuntu packages and install all the build dependencies successfully. But I haven't tried this yet on an active LMCE machine.
I need to change the Init_Build_Database portion to use a different name for the build databases so they don't overwrite the LinuxMCE databases. Right now the script drops those databases as part of the build process... As you noted it does not do anything with the MythTV database. The MythTV database is mostly built by the MythTV suite of applications when first run, so there is no need to initialize any databases as part of it's build process. For the LMCE build databases I'll probably prepend "build_" or something similar to avoid the name collision.
On a positive note, I'm trying the Kubunu + LinuxMCE install now, so if there are differences between it and the DVD install that affect the build process I'll be able to adjust the build scripts accordingly.
I'm happy to hear someone else is trying to build the thing from scratch, that's the only way we'll work out all the problems... I'm also very glad you had a backup!