In close to the same boat myself:
Though I don't still have any computers old enough to use my old parallel port programmer. And I'm just trying to get a new enough version of MIOS on my 18F452's that MIOS studio will recognize them.
I do have a pickit 3 though and it seems to flash and verify...but I get nothing out of it after :( Not even the MIDI data like you're seeing (even though I was getting it before trying to re-flash.)
I can help a tiny bit....This page: http://www.ucapps.de/mios_bootstrap_experts.html Has a diagram from TK on how to wire the pickit to the PIC: http://www.ucapps.de/mbhp/pickit_dip40_adapter_board.pdf
Hope you have better luck than I've had the past week with my pickit. If you do get yours working I'd love to hear how - or just send you my pic's to re-flash since you're only a few states away ;)