Nice one Marc.. These are mods I definitely had on the to-do list for my C11.. the fans should make a big difference.. as should the mirror locking bolts... That will definitely sort out any flip flop you may be experiencing..
Flocking the tube is a great idea too, but as far as the baffle tube is concerned, I'd be hesitant to spray paint in case of any overspray ending up on the primary (can you remove the baffle tube from the mirror?)
If the baffle is removable I would definitely give spray paint a go, I figure if you're already there with the scope in bits, might as well go all out, as I dare say you won't want to be pulling that bad boy apart too often!
Tell me, do your fans blow in alternate directions? or do you plan to have the air channel back out through primary baffle