First and foremost, I have zero Challenge Mode experience, so view everything that I say accordingly; I am, however, a fairly good Ret that tends to know what he's doing, so I'll do my best to offer relevant advice.
In my gear, which I do not intend to upgrade other than the heroic dungeon pants with a gem slot, I am doing 53k dps self-buffed in about 2mins on a target dummy blowing cooldowns. I feel that this is way too low for me, and too low for CMs. Any insightful suggestions after looking me over?
I open with Judge>CS>Exo>Inq, then blow CDs (HA, AW, GoaK, trink, pot), HoW>TV> then HP genys and HoW on CD, TVing when I can while keeping up Inq without clipping more than a second or two. Am I doing it wrong?
What's your PvP gear like? With MoP, Resilience and Power are on a separate budget from the normal secondary stats, so PvP gear works just as well for PvE - if not better, considering that you may have PvP gear superior to what you have for PvE.
Your hit and expertise are actually over-capped for dungeons; 7.5% of each is the raiding cap, while the dungeon cap is only 6%. That differentiation rarely gets made anywhere, as most PvE information is geared towards folks wanting to raid.
As to rotation, GoAK should not be stacked directly on top of any other CDs unless you're using Sanctified Wrath; with HA, pop Guardian first, wait about twelve seconds, then blow everything else. Because Guardian lasts 30s, and everything else last about 20s, all your
cooldowns will run out at about the same time, and the delay in GoAK also ensure that the angel-dude explodes while you still have Wings up.
Sort of an aside, I would recommend TV glyph over DS glyph, as we now have greater uptime on it since Exo was added to the proc list. As you're already glyphed for MassExo, this means you'll have a high-uptime passive 10% damage reduction even on AoE pulls.
I read on ElitistJerks that while pre-raiding, which is what I'm doing, gemming full STR is preferable.
Slightly misinterpreted, I think; EJ recommends strength-biased
gemming to certain, undefinable, player-specific gear points. You should not be mindlessly stacking any stat, as pretty much all socket bonuses are valuable to us this expansion (except hit and expertise bonuses, where they would put us grossly over cap).
With your gear, though, I think it would be safest to skip the socket bonus on the chest to make use of both your Serpent's Eyes, but swapping all other yellow sockets to Fierce gems would probably be better.
To clarify gem-biasing a bit, it is simply gemming with a specific stat in mind while matching sockets. So, strength-biased would use Bold red gems in red and prismatic sockets, Etched (strength/hit) gems in blue sockets, and, for Ret, Fierce (strength/haste) orange gems in yellows; Ret's haste-bias would use Quick yellows in yellow and prismatic sockets (unless you have no red sockets, then Bold Serpent's Eyes take priority for prismatics), Fierce oranges in red sockets (unless you have Bold Serpent's Eyes, which should always go to red sockets first), and Lightning (haste/hit) green gems for blue sockets. Even once you get to the point where you want a haste-biased setup, Bold Serpent's Eyes are superior to the Quick ones because of the way the Serpent's Eyes are weighted, each being an additive 160 stats instead of the double stats they were supposed to be; primary stats are still doubled, but secondary stats are only boosted by half.
I also feel like Retr is very clunky and unintuitive. Again, am I doing it wrong?
Haste would fix this, but if you're not aiming for more PvE gear, you'll likely never get to that point. Through the passive ability Sanctity of Battle, haste lowers all of our rotational ability cooldowns and our globals cooldown, meaning we can push more buttons faster for more frequent, tighter Holy Power dump cycles. You could try swapping your PvE gear to a haste-biased gem setup for CMs, since it might help to get trash down faster, but I honestly can't say for certain.
I do indeed have Seal of Truth up single target on the target dummy. I heard from an unreliable source that talenting Fist of Justice instead of Burden of Guilt and going Seal of Justice could increase my dps. How much merit does that have??
Whoever told you SoJ was a DPS increase over Truth likely had no idea what they're talking about. Truth is the damage Seal, period; Justice is primarily a PvP utility Seal. I do think FoJ would probably be the best talent to take at that level for CMs, though, as there are some healing adds in Scarlet Monastery and Shado-Pan Monastery, and some adds elsewhere that like to do some really nasty stuff.