Hi, here's my take:

Tuner, wah, TS808s, and Fat Boost in front of the amp.

Flange, trem, delay, and mm4 in the loop (Verberator).

FWIW, I use a Fuchs Tube-FX-Loop (the Verberator w/o the 'verb) in parallel mode.  I think you'll like it, I do!

Good luck.

JJ 6v6's might be able to take the voltages the OTS will pump through them, but I wouldn't risk using them.

As far as tonal differences, in various amps, I've found that 6v6's are nowhere near as smooth sounding as 6L6's.  In fact, the ragged nature of 6v6 overdrive is such that I can't stand using them for anything but early tweed Fenders.

The OTS has a great master volume, though, and in my experience, even with a 2x12 you should be able to get a good, low volume tone.  Of course, your experience and mine are different, & I hope that you find a solution.

Matched, both the ET-65 & Emi RWB are 8 ohms each.

I've owned my OTS since summer of '08.  Things I've come to learn:

I like the bias set a little "hot" on EL34 tubes (6L6's sound great, too, but I really like the EL34's)
I like the clean gain (first knob on the left) up at least 6 on the dial.
I like the treble & bass knobs a little lower than noon.
I like EVM-12L's, ET-65's, Eminence RWB's (right now I have 1 RWB & 1 ET-65).
I like closed-back, front-ported cabs (currently using a Hermida 2x12)
I like the amp at 4 ohms.
I like the OD section knobs at right around noon.
I like the PAB a lot, but I try to only use it for solos.
I don't like turning the presence knob up at all.
I like the loop ONLY with a Kleinulator or a Fuchs Tube-FX-Loop (currently using only the Fuchs)

I only play humbucker guitars with this amp, and I always have a Rocktron Intellifex going through the loop & Fuchs interface for flanged delay.

I've always only used the amp's OD with my OTS.  It took a little bit of fine tuning (layout, snubbers, cap values), but for rhythm and occasional leads, the OD alone is fine with me.  If I need a boost, I kick on the PAB.  For me, the trick is to set the clean gain up fairly high (5+) and make sure that the Fuchs Tube-FX-Loop is set to unity gain.

Dr. Ika? (Pickmaster), thank you, as I assume you were commenting on my rig/guitar.  Truly, this Les Paul is the most fun thing I've ever laid my hands on that doesn't have breasts!  The rig sounds great & gives me most every sound I have in my head, I'm very happy!

Well, nearly 1.5 years after getting my OTS, I think I've got my rig down. 

50w OTS (with all mods done by me)

Rack:
Furman PL+
Ceriatone C-Lator
Samson Airline wireless
Korg DTR-1 Pro
Rocktron Intellifex
2 space utility drawer

Cab:
Hermida 2x12" closed back, front ported
WGS ET-65
Eminence RWB

Guitars:
05 Les Paul Std w/Seymour Pearly Gates (neck) & JB (bridge), RS wiring kit, & TonePros hardware

Out front:
Dunlop Crybaby Fasel
SansAmp Midi-Mouse

You might check ebay, but, as the owner of a Gabkits head cab, I can tell you its VERY nice, quite sturdy, and looks GREAT!

Good luck.

I'm surprised to hear that the clean is supposed to be clean all the way 'round.  I play with the clean volume around 7, & with my Les Paul I can get a really beautiful, warm breakup by digging in.  I don't know if the Kleinulator has anything to do with that, though.

I've got my Winged C's biased at 37~38mA.  Headroom is good, but I run the internal trimmer low & keep the clean volume around 7.5.  OD Vol & Ratio is set conservatively, too.  I live on the OD channel with my Gretsch & OD + PAB with my Les Paul.

I debated a 1x12" combo cab from Gabkits, but lucked into a Fuchs closed-back, ported 1x12", so I use that.  I did buy a Gabkits OTS head cab, though, great quality, & its a looker to boot!  I've used an EVM12L in there, but I just recently went back to using a Speaker Warehouse E65 (clone of Celestion G1265).  It sounds...chewy.

Hey, Jonathan, here's my .02:

Its good that you decided to buy a prebuilt OTS, this would be a steep learning curve for a first amp build.

The combo cab looks really nice, I'm sure you'll be very happy with it.  I don't know what speaker(s) Nik offers, but the EVM12L & Celestion G1265 are across the board favorites with these D-type amps.

HRM OTS's have internal trimmers that control the Treble, Mid, & Bass in the OD circuit.  A "standard" OTS does not have these specific trimmers.  Both the HRM & non-HRM models will have a FET trimmer, a PI balance trimmer, and a gain trimmer that is only accessible with the chassis out of the head cab (or combo cab) - unless you ask Nik to add these controls to the faceplate or back.

As far as used OTS's, I've seen a few on ebay, & on TGP.  Good luck on your hunt!

Its always best to bias after a power tube change.

I lucked out and found a Fuchs 1x12 that I loaded with a EVM12L.  Great, compact package.  I was really tempted by the Gabkits.com 1x12 combo cab.  You might look into that.

What's a good range to bias then?