#1
Is there a particular order these pedals should be in in my chain?

Ibanez TS9, Big Muff, boss ds1 distortion
#2
depends what tone you're going for. experiment with different positions and you will realise that having more that one on at once, each time it will sound different depending on the order theyre in.
#3
ts9 first
i dont think the order of the muff and ds1 matters since you probably wont be using them both at the same time
#4
There's no correct way of doing this - it's a matter of whatever suits you best.

Even putting the TS-9 first is a matter of opinion - i'd be inclined to put it last if i was using it as a clean boost.
Live Rig January 2018

Fender Baja Telecaster/Danelectro DC-12
Boss TU-3, Ibanez TS9, Fulltone OCD 1.7, Boss CS-3, EHX Small Clone, MXR Carbon Copy
1964 Vox AC30TB with '69 Rola G12M "blackbacks"
Elixir Nanoweb 10-52 strings, Dunlop Jazz III XL picks