i have sent sysex with puredata for some years now, and i never had any problems, even with large chunks.

i have used attached abstraction to send sysex, maybe it helps?

midi IS a serial protocol, so it is perfectly valid to send one byte at a time at least over din midi. in fact i am doing that with arduinos all the time.  (usb midi is a different beast) 

do the “special” midiout noteon and noteoff messages work when a synthmodule or similar is connected?