Start by spraying silicone spray into the track the window slides in.
What the shop said about alignment is almost true...there isn't a way to align the front regulator, although there is in the back. But, there is slight play in how the regulators are mounted. I usually suggest that diyers use the 'shadows' from old regulator nuts to align the new one.
It's very easy opening up the door...just have some extra door clips around...and make sure the Vapor Barrier is sealed up tight.
There are many diys on this, and honestly, the silicone spray lubricant might help. If not, you can be confident enough on this that you won't mess up things too badly!
You need some basic tools...I think T-25 bit...and to remember to disconnect the battery 5 mins before if you're removing the air bag. Not sure you need to do that now to just, maybe, realign things...if you do get into the door yourself. (A plastic pry bar is nice to get the door panel off too--aka trim tools)
Upcoming NYC dates: Jan 8 and 27. See Facebook for other shows and PM me if you can make one...love to see you there!
Mangofy your E46!