I was curious since I also play as a Warlock in an Elemental casting rotation do I need to worry about clipping the flameshock dot? Or is the dps difference/loss irrelevant?

The Wiki has it listed as ~125 DPS.

http://elitistjerks.com/f47/t20914-s...lemental/#Sets

How much is the 4t7 enhancement bonus worth in terms of DPS? I rarely play enhancement, but since I'm usually the only shaman in the raid, I occasionally have the opportunity to pick up various pieces of gear and wondered whether they would be worth breaking up the set bonus for.

I was wondering if having+20 spell pen gem for a blue gem needed for meta's like chaotic skyflare diamond would benefit enhance shaman's for their shock spells and LB would work. And also wondering if the WF and LL procs were physical or magic damage cause LL is fire damage

You're still wearing some pieces from your elemental set so you should try to have the gear on similar levels before comparing.
Overall though it seams enhancement shamans beat elementals on most of the fights in Ulduar. (One notable exception is Vezax).
Since both shamand DPS specs are viable and bring invaluable raid buffs, you should definitely play the spec you feel more comfortable with and try to min/max your gear/spec/rotations.

Since spellpower has such a high value according to EnhSim and crit/hit/haste are hybrids, those elemental pieces are better or equal to anything I can get before Naxx25. My elemtal set is about the same level and according to the spreadsheets should give the same dps. I am thinking that it is probably just me having a hard time keeping track of multible cooldowns. Enhancement just seems harder to play and don't want to spend anymore time practising it, if elemental beats it further down the road anyway.

If I'm planning to level a shaman, would it be better to buy a Bloodied Arcanite Reaper for 1-80 or a Balanced Heartseeker and then another Balanced Heartseeker at 40?

We are also not built around fast weapons so the balanced heartseeker is crap for enhancement as well.

There are no good options for BoAs at the moment for enhancement past level 40. The reaper would work great till that point but once you get Dual Wield it loses appeal rapidly. Something like the Aurastone would be great once you get 5/5 elemental fury and switch from WF/WF to WF/FT but that won't be till you are in your 70s anyway so it is also pretty useless.

I'm having some problems getting a proper methodology for simming upgrades using either Rawr or EnhSim, mostly because of the fact that what items / gems are best will change depending on what buffs you have. We don't really have a constant / consistent raid makeup, and so I am having issues making a good baseline set of buffs I will "always" have.

What do you guys suggest to get around this?

Consistency could say to just turn on every buff and compare from there, or assume no buffs other than totems, and compare from there. However, that might not get me reasonable results as to what I should gem for.

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Separate question: Using Rawr Enhance v2.2.7.19935, Optimizer suggested replacing a lot of my AP gems with haste gems, along with swapping out a few pieces of gear -- I'm in that painful stage where I'm getting Uld 10 man gear that is a slight upgrade / side-grade but it's not worth it yet to break the T7.5 set. It simmed out as an increase in DPS, but I'm wondering if there is still any bias towards haste since the Levva coded the fix to 2.2.7's erroneous love affair with haste. Haste EP is still below 2 for me, whereas Crit is above 2 -- yet optimizer still suggested haste gems. I'll be trying a run or 2 with it's suggested setup to see how real world results fare.

I can provide the .xml file for Rawr if it helps narrow down any possible issues, but will have to wait for me to get home.

I personally compare results between all buffs and self-buffs. Going on self-only for 10-mans works simply because you will always have them; you can pretty much ensure that no matter what 10-man group you run with, your potential DPS will simply be higher than what you sim, if possibly slightly less optimal. It's a matter of logistics.

Normal breakdown except you aren't using Magma Totem and Magma Totem is a significant source of damage especially on Sarth with all the adds.