How to use SimCraft correctly?

Since EJ seems to be pretty well-gone as far as guides are concerned, I've been spending a lot more time fiddling with SimulationCraft. Unfortunately, though I have been able to obtain scale factors, I'm having trouble putting them to good use.

Could someone explain to me how to read/use the stat deltas in SimC? Regemming changes my scale factors for mastery/haste/int enough to change their priority, and finding the correct balance through trial-and-error will be unpleasantly time-consuming.
I'm not an expert or anything, but from what I've read on other guides (including ones on EJ) you want to gem/enchant before you reforge your gear. What I'll do is first run my character through SimC to get my scale factors. Then I'll figure out what gems to use manually with some simple math:

Lets say your Intellect and Mastery scale factors are 3.0 and 1.7 respectively. You'll want to multiply each one individually by the gem's stat. (ie; 160 * 3 = 480 for pure int, 320 * 1.7 = 544 for pure mastery, and (80 * 3) + (160 * 1.7) = 512 for 80int/160mastery) The higher the result, the higher its DPS value. So for this example you would want to use 80int/160mastery gems for red sockets, and pure 320 mastery gems for yellow sockets. You can check gems against all your scale factors to be sure. Also you'll want to add in the socket bonus as well to make sure matching colors are worth it or not.

Once you've gemmed/enchanted properly you can run SimC again and either take the new set of scale factors into a reforge tool like, or if you're patient you can figure out reforges yourself based on those new stat priorities. Personally I use askmrrobot. If something seems out of place I'll export the results to SimC to check how it performs in simulation before I actually spend gold on reforges in game.

Hope this helps somewhat. :)
My ideal reforges have remained fairly static, the issue I'm having is with gems. What will happen is that--for example--mastery will have a higher scale factor than haste, so I regem to mastery. However, this changes the relative value of the two stats, and haste ends up better than mastery at that point.

There's a "sweet spot" somewhere in-between, but finding it through trial and error is giving me a headache, and in the meantime my gemming looks like a complete mess.
Ah yeah I had that problem when I first started raiding except it was with reforges. It would tell me mastery was higher priority so I'd reforge mastery, then run SimC again and it would tell me crit was higher, etc.

Maybe you could try running SimC without gems to get scale factors based purely from gear and then going from there?
Aff will have significantly different haste scaling values as you approach and pass certain softcaps for haste. Non goblin 4717 haste is the most popular point to stop at whereupon you would go the rest to mastery.

Its also common for mastery to have a higher scaling value than int in terms of gemming budget. Once mastery passes half of int's value its time to change the gems. However if you are right at the tipping point and/or play another spec sometimes it may be best to leave the int ones in for now.

Hit cap is a more personal preference issue. Haste and mastery will be higher value than hit for most setups down to about 8-10% hit but again this can vary. Misses can screw a parse if they happen at a bad time and they invariably force you to spend more time focused on timers than on the fight. A solid rule of thumb is "hit cap for progression, max haste/mastery for ranking on farm content".
Thanks, Werst, I'll try working from that. I'm surprised that haste breakpoints still have an effect with the way Aff is now, with no real "extra" ticks.

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