In order to compensate the loss of the 4t8 you have to get at least 4 239+ items.

For instance this setup with late ulduar HM gear and early Coliseum this will make the trick and give you roughly a 50 dps increase :
Head : Hood of Lethal Intent
Spaulders : Garona's Pauldrons of Triumph
Chest : Embrace of the Gladiator
Gloves : Sunreaver Assassin's Gloves (232)
Legs : Legguard of Cunning Deception

No need to link to your Armory. We should be able to get it from your name.

Concerning your question, the spreadsheets (by default) model optimal raiding situations in a 25-man scenario. So if you're not reaching (or at least close to) the dps estimate in the spreadsheet, the usual standard questions apply. Were you receiving all the buffs that you enabled in the spreadsheet? Were those buffs up the entire time during fights or were they allowed to drop (i.e. DKs not renewing HoW, etc.)? If it was a multi-target fight, was there a full Sunder stack or an Expose Armor on your primary target? In a 10-man, there's a good chance that you are missing out on several buffs that would be assumed to be present in a 25-man, so make sure you model the 10-man scenario in your spreadsheet as closely as possible. Then try to check a WWS of the fights to see if the buffs you enabled were up the entire fight. If everybody else was doing their job, and your dps was still low, then the onus is on you to improve. Perhaps by managing or synching your cooldowns more effectively and maximizing your time on target.

Ah right, that makes sense, I forgot about the buffs part of le sheet -.-

But still, is there any reason that my DPS would go down when GT was put in place of Mirror of Truth even tho the spread sheets say it should be a decent dps increase?

You're probably not standing behind the target or attacking the target when GT procs for the full duration of the proc. The spreadsheet assumes that you are stationary and behind the target at all times, if you're not able to do so, you're not really getting the full benefit of the armor pen proc and the additional 83 hit that GT would provide would add little value when you are already at 330 hit. Therefore, having mirror of truth may work out for you more so if you find it difficult to stick to the target as the crit stat may provide a more immediate benefit. This is all speculation as I have no idea how you play. But based on your gear, on XT (one of the better fights to measure your dps as you should be stationary at all times given that you CLOS the bombs) you should see your numbers in range of the spreadsheet if you have the right raid composition and buffs. The spreadsheet is a guide and not law as mentioned several times in this thread as the spreadsheet cannot measure the skill of the player but do not doubt that the spreadsheet is modeling the DPS correctly.

I for one like to gem for expertise at times when my expertise numbers get too low as it makes it easier on my rotation maintenance. It's a personal choice and it does increase my DPS as it just works for me (i.e. rotation drops really messes me up)

ArP gets a nerf in 3.2.2 and you need 1400 rating to cap it. Does it have an impact to your best in slot and to the ruptureless cycle Aldriana?

Is anyone maintaining (presumably privately, since I haven't seen one here) a version of the latest spreadsheet math that doesn't remove the lower-tier gear, for those of us who are interested in the models but progress more slowly?

Pretty sure the nerf is still unconfirmed. It may be intended, it may also be a bug, and I think people have been reserving statements until we know more.

That said, I'm sure it does have an impact - how much of one, I'll leave to Ald to answer.

If you want to see the effect in the combat spreadsheet, in the Calcs sheet (in excel: right click Equipment at the bottom, Unhide..., Calcs) change 1.25 in B359 and B370 to be 1.1, and fill right across those respective rows.

At my moderate level of ArPen (594) it looks like I'm going to have to regem Agility at the very least.

Um, you need to change more than those two rows. Specifically, in the 1.2 sheet, you need to change all of 359-362 and 370-373. In 1.3 beta 2, it's 96, 846-849, and 857-860.

Some changes to be observed relative to the previously suggested BiS list. Changing the neck from Collar to Charge of the Eredar (258 Horde)/Charge of the Demon Lord (258 Alliance) is a dps upgrade and gems now need to be evaluated taking the socket bonus into account, sometimes making 10agi+crit superior to 20arp.
Axes are naturally superior to the dagger+mace combination now albeit only with some 65dps, abit less using Eviscerates alone. That's the most interresting change I guess; axe based setups keeps Rupture in the cycle (although not with as high uptime as previously), but mace+dagger performs best using Ruptureless cycles.

The "Use Agi Value for ArPen?" in the settings sheet is enabled by default.