#1
So my chain currently is...

Polytune mini -> Noise Suppressor -> GE -> OD -> Pre-amp Boost -> Dirt pedal -> looped back to the Noise Suppressor -> Delay -> Phaser.

I am thinking the sustain should go between the polytune and the noise suppressor right at the start.

Also I own two ODs. The one in the chain I use to tighten the sound so the gain is set to 0. I would like to use an OD with the gain up so I have a second OD. I have sometimes placed this at the end of the chain after the phaser. However I am thinking maybe I should have it next to the other OD. So which first? The OD for tightening the sound or the OD with the gain? Or any comments welcome.

 
Dean MAB1. Epiphone Annihilation V. EVH 5150III. Orange PPC112. Earthquaker devices - The Warden, Arrows, Acapulco Gold, Levitation, Night Wire. TS9, DD3, GE7, NS2, LS2, Polytune mini, Small Stone. SM57. Focusrite. LINUX!
#2
OD for tightening first OD for gain second. this of course assumes you would be using them both at the same time otherwise it makes little difference. 
#3
I know very little about signal chains.  However I was taught early on, and has been my operating philosophy, to keep it simple in terms of thinking about them. 

There are two types of pedals as far as I'm concerned: effects that change the sound of your signal, and effects that boost/amplify/drive your signal.  For example take a guitar/amp and first run an echo - distortion, then run distortion - echo.  Fundamentally, option one means you're taking a dry signal, modifying how it sounds, then distorting the modification.  Option two means you are distorting your dry signal then modifying that distoted signal.  Pretty basic stuff, again I know very little.  

All this said, your question for me boils down to this : tuner -> suppressor (loop -> eq - od - pre boost - dirt) -> delay -> phaser ; where can I put my extra OD?

Basically, the overall signal chain doesn't matter, the fact that you use a supressor loop doesn't matter.  You've chosen option two: distort your signal then modify it.  Which brings us to the point (after all of my wordy attempts at applying logic to the matter): do you choose to drive your signal then tighten it? Or tighten it then drive it?  Both are valid.  The accepted route is stated above (Tight OD first then gain OD second).  People like this method the most because the contrasting option will condense your distorted signal and you'll end up feeling like you need yet another pedal (which btw is probably why you feel the need to run a supressor with an eq, od, boost, and dirt)
"I definitely don’t write all my music in a blackout, like I used to, although I did come up with some good stuff in a blackout."
-Matt Fucking Pike