Amplification:

•  Mesa Boogie Mark III Long head
•  Two felt-covered 2×12 cabs
• 
Bogner Shiva combo behind stage is plugged in and may be more than just backup
• 
Leslie G-37 rotating speaker

Guitars:

•  1996 Koa (chrome pickup covers removed).  Note: Trey told Jambase the following about his guitar for Summer 2015:  “I replaced the pick ups on all my old guitars with double space single coil pickups that fit into the existing space where my old humbuckers used to be. And I was able to use that single coil sound throughout last summer.”  This may explain why the chrome covers were removed.  Most single-coils are lower output than PAF-style humbuckers, and the covers would only mute them further.  Commenters have suggested these may be Seymour Duncan Stag Mags, which seems plausible.

•  Ocedoc.  This guitar was used in the latter half of Summer tour, including Magnaball.

Floor Pedals:

•  Digitech Whammy II
•  Boss OC-2 Octave
•  Beigel Soundlab Tru-Tron3x Envelope Filter
•  Dunlop Wah
•  CAE RS-10 Audio Switcher
•  Boomerang Phrase Sampler
•  3x Boss FS-5U (“Once” sample for Heavy Things, Leslie On, Leslie Fast/Slow)

Rack Pedals:

•  Tube Screamers (note: no Analogman Sunface logo on these)
•  Shin Ei Uni-vibe
•  H&K Tube Factor
•  Supa-Puss analog delay
•  Alesis Microverb (reverse reverb)

Rack (from top):

•  Furman PL-PRO DMC E Power Conditioner
•  Korg DTR-2 Tuner
•  Ibanez DM-2000
•  TC Electronic D-Two3 x CAE 4×4

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Ocedoc at Magnaball (via Ithaca Journal write-up).

OR head on
In this shot from the Oregon show (7-21-15) he Mesa Boogie is behind Trey to his right.  The felt covered 2×12’s are stacked horizontally behind him.  The rack sits above the Boogie, and above the rack sit the rack pedals.  You can clearly see the green Tube Screamers from this angle.

8-4 nashville overhead
This overhead shot from Nashville (8-4-15) gives us a good angle on the pedals sitting on the rack.  The Univibe is slightly cut off at the top right.  Below it you can see the series Tube Screamers and the H&K next to them.  This also gives us a clear shot of the floor array.  From Trey’s left, you can see the Tru-Tron (in white), then the Whammy II and Octave pedals , the CAE switcher, the Boomerang, and then the wah.

8-1 ATL rear
This angle gives us a clear look at the Leslie G-37 and the Bogner Shiva combo, which is plugged in but not mic’d.

rack close up
This shot from Grand Prairie (7-29-15) shows the top of the rack.  You can see the Tube Screamers, which in this case do NOT have Analogman sunfaces.  Behind them to their left, there’s a Way Huge Supa-Puss (it’s the blue pedal).  You can also clearly see the chrome covers have been removed from the humbuckers on Trey’s ’96 Koa.

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Here’s a look at the staggered pole humbuckers on Ocedoc.  It’s unique for a humbucker to have the poles exposed through holes in the chrome cover.

bogner plugged in
As they walk onstage 8/22/15 for Magnaball, you can see the Bogner Shiva head is clearly plugged in and powered on, in addition to the Boogie Mark III.