Also have a question on the same subject... The specialtech rubber says maximum thickness should be 1.5mm on the panel while the only acrylic they sell is 3mm thick... Would that work out or would it look really ugly?
Not too sure why you'd be putting U-channel on the acrylic?
Might be missing the point, but as the acrylic should be hidden on the inside, it shouldn't really need covering up.
It's normally used for the metal side panel after cutting to save on filing.
Sorry mate didnt actually figured out your plan. I think putting u-channel on a thicker edge then it was initially designed for will not work properly.
So try to find a model that suits thicker panels.
Like this for example.
http://www.gummi-plast.de/product_info.php/info/p8077_TU1-0186_Rubber-Profiles.html
Or this.
http://www.gummi-plast.de/product_info.php/info/p4922_TU1-0605_Rubber-Profiles.html
Couldnt you just cut them off, then file untill you get a clean result, put u'channel on the entire cut-out and come from inside with the acrylic and double sided tape.
Looks like there is enough space to tape it down.
Just take your time when masking the acrylic sheet. Also sand the area that will be painted to get a good adhesion, i'm not a painter but i would use 600grid . 2 or 3 coats should be enough, be sure to paint in a well ventilated and dust free area (for a good finish and your health!)