Modifying your sump shouldn't be to much trouble, if you trial fit stuff and precut it all before you glue your system shouldn't need to be down for more than 24 hours. Once you have that baffle system you can add an auto freshwater top off like the Kent here
http://www.jlaquatics.com/cgi-bin/sh...no=ro-kpfvalve I doubt your system will suffer from 24 hours with out a skimmer. If it's really a concern do a good sized water change first and don't feed your tank during the 24 hour period. As far as the acrylic goes, just any fibreglass/plastics shop should be able to help out.
Doug