You're correct that waiting for the 3rd stack of Thunderstruck is a net DPS/threat loss, compared to just using SW a as it comes off CD. Another reason this is true is that using TC more than you have to is a net DPS/threat loss aswell - even considering all factors. So it's partially because a waiting for the cooldown on any ability is bad - and partially, because using TC when you don't need to, is bad.
This is true in both single target scenarios, and multi-target (nothing changes). The only difference is that in a multi-target scenario you're going to be using TC as part of your AE rotation, thus yielding more Thunderstuck stacks. It's irrelevant to using the ability as it comes off cooldown though.
The glyph is also irrelevant. It only dictates how many GCDs you have to wait in between uses. You still use it as it comes off cooldown, without regard to Thunderstruck stacks, regardless of Glyph.
I also have to disagree with you on the last paragraph entirely. If you do not need the interrupt for Heroic Throw, keep the points in Thunderstruck. You're replacing that 2nd Heroic Throw with Rend once per minute, and is nearly equal to the increased damage you would do from Gag Order. If you Rend one additional time per minute (total of twice per minute), Thunderstruck surpasses Gag Order for single target DPS/threat.
I'm not sure why you have 1 sentence about Glyph of Sunder Armor is in there. It's totally out of place. (and the wording doesn't agree with me - I'm pretty sure LK can be done without the Glyph of Sunder.)
Heroic Leap (as of current build) no longer stuns.
There seems to be some misinformation on your website. Specifically the single target rotation page (http://img21.imageshack.us/img21/566...orityfinal.png). Similar to what I said in my first paragraph. TC should only be used as absolutely needed. If you have another raid member providing the attack speed slow debuff, you can take it off your bars. On your single target rotation you should not be prioritizing TC over any other ability in your spell book (except to maintain the debuff). TC has about the same priority as Demo Shout. The only exception is if you have a Blood and Thunder build, and you're refreshing Rend via TC.
Also, assuming I'm reading it correctly (I may very well not be), it appears you have 16GCDs worth of abilities there, but only 3 Shield Slams. Discounting Sword and Board procs, there should be a minimum of 4 Shield Slams in a 16GCD period. For example, your first TC in the rotation should not be there, except if providing the debuff (everything would move up 1 spot). Also, the "Thunderclap X2 TS" should be a Shield Slam - as it has been 4 GCDs since the last SS.
Too much TC, not enough cow bell - I mean SS.