The Martin strings are great. Just have the action set for that brand and the gauge you use; most techs will do it for between $35-$50. Fret dressing is a little extra, but worth it. Refretting is a whole 'nother deal, of course, but it changed my whole acoustic sound. I highly recommend it.
The Baggs pickup is more current than my knowledge and is certainly the way to go. I would still take a hard look at that internal mic in addition. It adds a dimension that no pickup can. You're already used to running two cords, so if you can't get it as an integrated install (but I'd try, using a three-conductor end-pin jack and cord) you're ready to go.
Mac's comment about the phase shifter surprised me, but I rarely doubt him. Each level of time-domain effect--phase shifter, flanger, and chorus--is characterized by a longer delay time and correspondingly smoother sound. I've never heard a PS that smooth--I'd love to know who makes it. Anyway, look up Chaquico's acoustic rig; I am certain he will have good pointers for you.
You're asking the right questions. Keep at it and one of these days we'll be looking up your rig.
R.