i don't believe bubbbles are an issue, but i am not an expert and i'm sure there are more knowledable people on here, but for flushing the tranny? special tools? naw, just some knuckle busting (possibly). you can always do the flush/removal of trans fluid thru the cooler lines while the truck is running. i've only done it on vehicles (at work) that have dirty fluid that way i know when it's clean cause the color/cleanliness of the fluid come out of the cooler lines. BUTTTT, if i'm
changing fluid on my personal vehicles, i change everything.... filter (and seal if applicable), fluid, pan gasket (if need be). but that is just me. some people are perfectly happy just flushing the stuff out instead of changing the filter and whatnot. Since you "should" have a new filter and fluid, there would be no point in doing all of that. but with an old filter, why try pushing new fluid thru a dirty filter?
just my $.02
personally, if i was you, i wouldn't worry about bubbles if the fluid is at the right level and just changed. but hey, mabe the tranny experts will chome in.