As for the Companions issues, if they exist, I don't think it'd be too difficult to fix them; the main problem is identifying them in the first place.
Reporting back about the Companions issue (forced removal of followers as part of a quest script). After testing both quests (Silver Hand and Purity of Revenge) multiple times, there are no issues.
I tested w/ 3 followers and what happened was they were never removed by the quest system (ie all of them came along from beginning to end of both quests).
Spoiler
In Silver Hand, all followers followed me into the Underforge. Then all disappeared during the Werewolf transformation (no alias removal messages appeared on screen). They then reappeared at the target destination w/ Aela after transformation.
I also tested dismissing and rehiring all followers immediatedly after each quest to see if the alias enumeration was affected in any way. All were correct and working properly.
Edit:
A thought regarding the NPC outfit issue: is it possible to replace the default outfit of the follower with an empty LVLI, and then assign the default clothes/armor to that LVLI on dismissal and remove them upon hire? The functions are there, only problem is somehow maintaining a map of each NPC's default clothing.
Remember that mod conflict I linked earlier in the thread? http://skyrim.nexusmods.com/downloads/file.php?id=8530 That is another quality mod that solves the "NPC clothing issue". I think he replied to your post, maybe you guys can work w/ one another. And about the "default bow issue", please include a fix in the next revision. I don't consider these two issues "bells and whistles", they are bug fixes and they are entirely appropriate to be integrated into this follower mod.
Foobar, here's a link to that thread: http://www.gamesas.com/topic/1346637-rel-tcg-tradable-companion-gear/