You've overcapped armor penetration in the first set by 6 rating; you could say you'll only get 14 arp from one gem. I would suggest using one strength gem instead: 3,74*14=52,36 vs the 20*2,87=57,4 from one Bold Cardinal Ruby. Likewise in the 277 set but you're only overcapped by 2 rating, making the arp gem still better than a strength one.

You will most likely get an infraction for violation of rule 7, so in future feel free and test it yourself. I'm quite sure, you would've found out, that both of your question are, no offense, redundant. But as I don't want an infraction for disregarding rule 10, I will still answer your question, because this wasn't already discussed in the thread and this leads to some answers, which may interest several other people as well.

So, coming to your first question:

You suggest eating 40 ArP buff food and socketing 40 Strength over eating 40 Strength buff food and gemming 40 armor pen. You end up with 40 ArP and 40 Strength either way. There's one exception for the 264 gear: If you're a JC, and only if you're a JC, you can replace one 34 ArP gem with a 34 Strength gem resulting in 40 ArP food buff plus 34 Strength gem versus 34 ArP gem and 40 Strength buff food. This gets you closer to the cap without overshooting it. Will update the 264 Set and add a note to clarify it should be used with [Hearty Rhino].

Second question:

Gaining 45 armor pen rating from an elixir, swapping gems for not overcapping, results in effectively chugging 40 Strength and zero to five ArP rating. Best case scenario 40*2.9+5*4.5<180 still favors AP flask, however if you're sitting at 1,200 armor pen (with Bryntroll heroic e.g.), [Elixir of Armor Piercing] could be superior to flasking, but only individual sims will show this.

Anyway, I completely forgot to add buff food and flasks in the sim, redoing APEs now.

While I am at consumables: This is no longer true, AP is now also updated on armor value changes.

In the WOL you linked autoattack is close to 70% of the DRW's total damage. Furthermore, the average crit is showing at almost 9k - the max crit would be even higher. Another thing to consider is that in most cases the first DRW you cast will be with the most procs up at the same time - things like the Ashen Verdict ring, and DBW throw proc alignment out of whack because of their strange ICD's (i.e. not 45 seconds like most trinkets).

It's pretty clear that DRW is gaining some benefit during the BQL encounter - there is no other explanation for 12k DRW crits when the norm for top of the line ICC gear is 7 to 8k max.

Going back to your original question - is it worth swapping out glyphs? My DRW on Festergut Heroic this week was almost identical damage wise to my death coil:

Festergut

However - GoDD's worth is easy to figure out - it would've added 15% more death coil damage. However, GoDRW is an additional 5 seconds (on top of 12) for about a 42% increase in duration. It's not as simple as a 42% damage increase however - depending on the DRW's attack speed, you may lose out on an autoattack, and the last 5 seconds may not have consistent ability usage due to rune cooldowns and lack of RP. It's pretty obvious that it would be much more than a 15% increase, however.

Honestly, I welcome additional discussion on the mechanics of Rune Weapon - it's one of the most misunderstood abilities in the game at the moment. I'd like to do some additional testing myself to verify some of its behavior. We know it scales with Haste, AP and Strength. The general consensus is that it does NOT scale with armor pen, and I've seen arguments for both sides on whether or not it scales with crit rating. Furthermore - some people insist it doesn't scale with Hysteria or Blood Presence, and some insist it does. I haven't seen convincing proof either way, however.

And finally - it seems to scale to 50% of your autoattack damage (minus armor penetration most likely), however the rest of your abilities aren't affected by talents or glyphs, which ironically makes death coil one of the hardest hitting abilities to use while Rune Weapon is active because it is already the closest to baseline (as opposed to several talents and glyphs increasing heartstrike and death strike).

We've already been over DRW and why autoattack makes up the majority of it's damage output.

Your simming is flawed:

1). You're using a generic gearset that was built for unholy - it only has about 800 armor pen. To accurately sim blood dps use an armor pen gemmed one close to hard cap (you can reference my armory and use my stats). This is a several hundred dps loss and not accurate.
2). You're probably using the default GoD spec in kahories which takes a point out of epidemic and moves it to morbidity which would inflate death coil damage. This is a several hundred dps loss.
3). You probably have the wait for procs to use DRW turned on and are using a 45 second, 60 second, and 75 second ICD items -this will make the sim wait for these to line up before using DRW which kills it's uptime. This is also a several hundred dps loss, and would lower DRW value compared to DC.

Furthermore, I have my doubts that kahories models DRW correctly - it consistently undervalues it dps contribution. In game parses generally are well above the ~4% total damage it reports.

Rerun the sim correctly and see what results you come up with but it's pretty clear that currently GoDD is not worth trading for GoDRW. Your assumptions so far have been incorrect - with the exception of whether or not DRW will scale with the ICCraid buff which is currently unknown.

On a related note, the general consensus for GoD is to reapply diseases when you pop DRW so it will have it's own diseases - this appears not be the case. Last night I found out that if you have diseases on the target, use DRW and then hit pestilence, your diseases will refresh and DRW will also use pestilence and put it's own diseases up without them previously being applied by it/ps.