Yes, you could extract modules from the 3.9 ROM update, but then you'd need to issue a reboot during bootup to get them kicked in [though I see you're using BlizKick anyway, so maybe that doesn't matter]. It also takes you into NSD territory, which requires that annoying Devs:NSDPatch.cfg file and possibly another reboot. The 3.9 HDToolbox will also need a whole mess of Reaction classes and libraries, which might get very annoying to deal with on floppy.
Bottom line: Using 3.9 modules is possible, but TD64 preserves the simplicity of a 3.1 installation.