Hello,
I would like to record a midi file with a combination of [notein] and [makenote]s in PD. Do you think this is better done by routing the midi data to another application to record, or by using some PD external (currently unknown to me) that can record a midi file directly in PD. Any suggestions or help would be greatly appreciated!

check out 'qlist' and 'xeq'

Thanks! I'd like to use 'xeq', but I am using a mac, and I can only find a linux version to download. Do you know if anyone has compiled it for Mac?

Try one of Hans newst builds, maybe it's in the Mac build now...
http://at.or.at/hans/pd/installers.html

It looks like it's not it in the Mac build yet, but thanks anyway.