Operator Thogar
All aboard the rape train WOOOO WOOOOO!!
This encounter is very much an add-based fight and is almost entirely about managing incoming trainloads of various add groups within short time periods before the next trainload arrives and steamrolls over the raid.
Addon
Per Tree's post, @everyone should install the Thogar Assist addon: http://www.curse.com/addons/wow/thogar-assist
It seems to be the better maintained and put together of the two addons for this fight (and also looks nicer, which is an added bonus).
Trains & Tracks
The primary gimmick to this encounter is of course... DE TRAIN! DE TRAIN!
There are (4) parallel tracks running through the encounter area and frequently throughout the encounter, trains will pass through along a track and quickly exit the area, or the train will stop and release a number of mobs to be dealt with.
Normally I'd dig in and write down the key events of the trains, but since that's already been done for us and is presented in such a lovely addon above, there's really no need.
Group Splitting
On approximately one (and technically a half) ocassions during the fight (at roughly 2 minutes in), (2) add trains will appear simultaneously in the two central tracks and spawn adds out from the opposing sides.
Solution: The raid must be split accordingly to deal with each set simultaneously. One tank will retain Thogar of course, so that side should have the majority of healing.
Notable Train Adds
Gunnery Sergeants are likely the most critical and will remain on top of the train, firing Delayed Siege Bombs and a specific, targeted player for a few seconds. These bombs detonate after 30 seconds dealing moderate damage to anyone within 9 yards.
Solution: Individual player(s) targeted by the Gunner should move out of the raid, along either opening door wall to drop Bombs out of position of most of the raid, allowing them to explode safely. Worth testing: Will stepping onto a Bomb preemptively cause it to explode and if so, can immune or 90% reduction players purposefully do so to a large clump of Bombs?
Cauterizing Bolt is an interuptable heal cast by Grom'kar Firemenders.
Solution: @Melee DPS in particular should be prioritizing these mobs when they appear in packs. Firemenders spawn in pairs along with others in that pack type, approximately once 90 seconds into the encounter and again around 3 minutes later. Interrupts to stop the casts are ideal, though the heal once applied lasts 10 seconds and can be Purged via offensive magic dispels. Worth testing: Stunnable?
Operator Thogar
Enkindle is the primary @Tank-swap mechanic and applies a stacking DoT for 25 seconds, dealing 10,000 Fire damage every second.
Solution: This ability looks to be used every ~12 seconds, so tanks can swap every 2 stacks without much trouble.
Pulse Grenades are thrown at random ranged players and deal heavy Nature damage for 20 seconds in that impact area. They also draw players toward that location.
Solution: Ranged/healers should try to remain near max range from melee and be quick to move out if a Grenade is thrown nearby.