Suggestions on the colored transoms....
Large crafts-oriented stores....Michaels, JoAnn's Etc., Hobby Lobby, etc....often have colored transparent gel film in squares about 10" or so, multiple colors. Laminating/substituting a strip of this in the transom area might help.
Similarly, there are clear paints (Tamiya, Testors, et al make them) in a few transparent colors that can be applied to the inside of the transom film area. I know for certain (work at LHS) that they make an 'amber' (orange?) in support of the automobile modelers. An experiment mixing red/blue might also give you a suitable 'purple' for this application....perhaps.
Somewhat surprised that a marker pen of the appropriate color didn't work, though. That would've been my first attempt, too.
Looking forward to your build!
KD