I've done this using a print tray, Trey (couldn't resist). Lay the film strips in the tray base side down, add solution, and agitate gently. I hang 35mm strips on hooks fashioned from paper clips -- looks like you're doing something similar to weigh the film down.
ETA: Rereading your post, the soft emulsion side is more prone to scratching than the base, so as long as the emulsion side is face up and the film strips have some room to move around in the tray, you shouldn't have to worry about scratching or damaging them. Make sure the tray bottom is smooth just in case.