Ok, so first, there's the copout answer, here's a guide:
http://www.stoacademy.com/guides/crafting.php :laugh:
Now that that's out of the way, it really depends on what you're wanting to accomplish. Honestly the R&D system is kind of worthless in the long run, it was really awesome when it came out as it dumped some new items into the economy, made RCS and Particle Generator consoles useful by creating special new versions, and made many weapons more accessible. Now, the only real useful thing it does is provide upgrade fodder, and/or make mk xii gear easier to obtain than in the past.
If you're wanting to make R&D useful for creating stuff for your ship/crew, then focus on what you want, and put everything in to building up those appropriate schools (you can queue up to 3 of the 6000 XP missions on the same school in a single day). And then craft the stuff that you want. Something to note here, if you are crafting the Mk XII stuff, you'll need purple components, don't craft them, it is such a dilithium sink, and given how many R&D packs have flooded the market between the Sheshar and Strike Ship promos, plus they drop from lockboxes, buying the purple components outright off the exchange is just a much smarter move economically.
If you're wanting to use R&D to make money... good luck? You can make some major bank, but it takes a lot of patience, and a lot of frustration as you have to junk a ridiculously massive amount of items. There are only a few things that are worth like anything that pop out of the system, and the ones that are worth the most also have the biggest risk associated with them:
The Conductive RCS and Exotic Particle Field Exciter: most of these are worthless, even at ultra rare. If they have the [EPS] modifier, you'll make a killing, if they have other moderately useful modifiers like [turn] [shhp] [prtg] or [resall] they can be worth between 3-20 million. Everything else sells for less than the materials you put in to them, so it's a big gamble (and not worth attempting until you're at level 20 in that school anyways)
Weapons! If you grind, you can keep pumping out mk ii (yes 2) beams, looking for either [dmg]x3 or [crtd]x3 as the modifier on the weapon, and they will sell for 2-8 million EC. It's a guaranteed way to make money, you'll never spend more than you make. You'll also go absolutely crazy and hate the game.
Honestly, the best thing to do with them is wait until the upgrade weekend, then open them, and sell the upgrade accelerators contained within. The prices on them will spike as everyone tries to upgrade stuff during the bonus period. That, and then use the parts inside to craft SUPERIOR upgrades and sell them too. At this point, the R&D system has outlived a large part of its usefulness for the majority of the playerbase. If you're not wanting to grind, then chop those puppies up and sell the pieces. If you are wanting to grind, let me know and I'll give you the tips necessary to do it, I've spent plenty of time doing it myself, but I know that's generally something most people aren't excited about :)
Good luck!
