ARC Cody, I can answer a few of those for you.
The Sion Peragus Arrival mod wasn't included as it would double the size of the download. It should be compatible with the TSLRCM however, so feel free to add that one in.
Look to Varsity Puppet's upcoming "Malachor VI" add-on to correct that issue where the Marauders and Lords on Malachor V look like civilians.
As for the TSLRP bug fixes, I don't have any answer on that. Perhaps Zbyl2, Hassat Hunter (or any of the beta testers) might be able to clear that up.
As of 23JUN13: I released a new small texture mod! Check it out here