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sorry for being later than late.

though, i'd still answer each one of your questions in very brief manners... sorry for that.

1. Play 1 to 16 tracks to 1 of 8 audio outputs via Jack or ALSA? Midi tracks using Jackmidi or ALSA?

while on qtractor's Files widget, usually the right-most pane, you probably missed that, besides a media content file organizer, it's also a media file player: it can play complete audio files and MIDI files as well; audio files are enqueued for audition on the first output audio bus, usually Audio Master Out; MIDI files, all or one channel or track, (depending whether it's a SMF 0 or 1) it will be sequenced or play through the first MIDI output bus, MIDI Master Out is the default.

that said, it all depends on whether you have those master outs connected through; the special case for the MIDI file player you ought to know that it needs a sound-module generator to render the MIDI evenets that are being spit out--eg. old GM multi-part/timbral synth, sampler, ROMpler, comes to mind here: fluidsynth, qsynth, timidity, etc. GM/GS/XG capable external equipment is on demand here ;) personally, I have always have a DB50XG nearby, just in case you missed one of my other gems (qxgedit.

2. Must be able to remote control using a external connection via ethernet port or midi I.e.
A. Use a OSC app iPad to load next song or song number from a remote connection via network port, able to stop, start, next previous, loop markers transport control through app and local control.
B. Use raw midi bank sel cntrl 00 & cntrl 32 & program change to select and load song. First 3 digits in song name before '-' . There may be a better approach. Transport control using note on off or cntrl assignments.

well, now you got me stranded there. the audio/MIDI file player feature mentioned above is not accessible or controllable from the outside, not even by MMC as the general qtractor transport controls are.

3. On each song load ability to auto play however, send program changes ,midi messages prior to track starting? Could use a midi raw flat file for patch assignments. May ask why, external keyboard and midi dmx lighting can load correct patches before starting song. Always been an issue live.

that seems to be an issue for the target sound-module/generato, synth, whatever, for which i referred on 1. qtractor does not incorporate any of those things. sorry.

4. audio and midi track channel output group assignments config stored in xml file included in song project directory.

the so called qtractor sessions does exactly that, i believe, when you load a multi-track/channel MIDI file: for SMF 0, each MIDI channel becomes a qtractor MIDI track, while on SMF 1, each MIDI track becames, obviously, a qtractor MIDI track.

however there's no such group concept in qtractor, other than each MIDI track may be assigned ie. routed to separate MIDI output bus.

5. Able to store loop points to replay a section within a song between markers and able to play into the section then loop back to a previous marker until told to play through. I.e. Play 16 bar section continuously.

ad-hoc vertical loop/cycle-points is currently possible in qtractor; vertical in the sense of the time-line, across all tracks; however it loops in there forever or until you act on it (loop (re)set). what you ask is probably something that i've been thinking about, something like a pattern-based, programmable/scriptable looper/sequencer that take location markers as its heart; never mind, it's still in my thoughts; not implemented yet. sorry.

cheers