Ay, I got it to work.
First, I removed the -msse flag.
Then I added a comma with no space after the -Wl flag.
Finally, for some reason, the helmholtz~.cpp file disappeared when I copied the src folder onto the Pi.
This is where that "helmholtz_tilde_setup" is referred to, so although the helmholtz~.pd_linux object compiled even without that cpp file, it obviously wasn't going to work.
Once I copied a fresh copy of the helmholtz~.cpp file into the directory, it compiled fine and now works like a charm.

trevor92 - Any chance that you remember what you needed to change in the makefile to get helmholtz~ to compile successfully on your Pi?
I got it to finish compiling by removing the -msse and -Wl flags, but I can't get the resulting helmholtz~ object to load in Pd.
I get the error "load_object: Symbol "helmholtz_tilde_setup" not found" followed by a "...couldn't create".
I've double-checked my path, so I'm assuming the build is the problem.