I chop up racks all the time and usually just do it on-site with my Bosch jig saw and a speed square.  Something like a SRSR or SRS only takes a few minutes to shorten the rails. 

I keep a can of satin black spray paint in the van to finish the ends and keep them from rusting.  It works best to spray a little paint on some card board and then dip the end of the rail into the paint instead of trying to spray the end of the rail which gets messy.