3000 - MIDI Networking with hardware - best way to setup?

So I have my 3K with 3.5 and a CF reader. I currently have it networked with a DX7, a Sub Phatty, and a 106. I also have a 'master MIDI controller' and a MOTU MIDI Express XT.

Basically, I want the 3K to be the master, but here's some other functionality I'd like. Maybe someone can help me figure out the best way to set things up:

1) I want everything to be connected to the MPC with both MIDI IN and OUT, since things like the Sub Phatty can transmit CC when knobs are turned, and the DX7 can send Sys Ex, etc..

2) I want the best timing, so I wonder if the merging software in the MOTU is going to work against me there -- in which case, I'd rather not use it (if it introduces latency)

3) When working on a particular Track on the MPC, I'd like for it to be able to receive MIDI from both a) the active track's corresponding port / connected instrument, and b) always from the 'master MIDI controller'

4) I'm not too concerned about sending MIDI from the Pro Tools / Logic. I can always dump MIDI tracks from Pro Tools on to a CF card and put it in the MPC.

I think the best way to connect your set up would be to connect each of your hardware synths to a different midi out port of your MPC. Having 3.5 allows you to send midi clock out of all 4 ports - better sync. Connect your midi master keyboard to the midi in port. You should be able to control all kinds of parameters (filter cut off, sustain, pgm change etc.) of your synths through a single master keyboard mapping CCs or sysex. You can even choose to connect one other synth to your 2nd midi in port. Midi in from both keyboards will be merged. A master keyboard can be programmed to send different knob movements or buttons through independent midi channels or even split the keyboard to do the same. I guess the only limitation here is that the MPC can only receive midi through the active track, and the active track can only send out through 2 ports/2 midi channels simultaneously for live manipulation of synth parameters for example. If you want to control synths live or record knob changes I would set a track apart routed to the 2port/2 channel option and leave that as the active track while the song is playing.
I don´t see why you would be sending midi in to the mpc from Pro Tools unless it's for sync purposes. In your set up you still have a free midi out port to control virtual synths in your Daw if you chose to.
Hope that helps...