I personally prefer Quantum torps in space; for the higher burst damage and the fact that they travel faster... buuuuut ultimately it's a matter of preference; photons work fine too. Plasma, Transphasic, and Chroniton are all kinda 'meh' imo though.
I do want to make a quick note on the Tricobalts though: They can be potentially very useful; however I'd never actually put points into them. The key thing though is that imo, they're best used on an Escort in the back. The idea being that you make your pass, pull a fishhook turn away from the shield facing you just obliterated, and then dump a Tricobalt on your way out. Strictly speaking it's probably less effecient than using Quantums... but it is a lot of fun imo. (And since it requires no skill investment, you can always try it out for kicks with no guilt.
Lets see what I can do on the rest of your points >.>b (Glad this is useful to you!)
2) - Honestly, all 3 top tier cruisers are fine. I personally prefer assault, but that's mainly because I find the 3rd ensign Engineering power on a Refit Explorer a bit redundant. That said, redundancy can keep you alive; and the saucer separation can be a lot of fun in the right situation.
Actually outfitting them... this depends, there's a few different ways to go:
There's a full on beam boat (4 arrays forward, 4 arrays rear) - basically just broadside like crazy and they will die. Not my cup of tea so I don't have a ton of experience with it. My understanding is that Fire At Will is a good choice for this kind of ship though.
Then you've got your mixed beam boat - 3 arrays forward, 3 rear, 1 torp in each direction. Idea being to broadside as per above, but twist to hit them with torps as needed. Tried it, personally didn't like it. It wasn't that it was bad, I just hated having to swap facings for the torpedoes, even though it wasn't a big deal.
My personal setup is like the mixed beam boat, but with a dual beam bank up front instead of the 3rd forward array. The advantage here is that my forward firepower is increased, and thus I have a good reason to keep my nose (and my torpedoes) on target. The disadvantage is, I sacrifice a little broadside power. Ultimately I find this a worthy tradeoff, but it really depends on how you like to fly your cruiser.
Then you've got the Turret or Turret and Single Cannon build - I've got a character who uses this as well actually and it is quite effective. The setup I use being 3 Single Cannons up front and 3 Turrets in back. Obviously Rapid Fire or Scattery Volley are musts. (Sadly unless you've got an Excelsior, it's one or the other.)
The fun thing about this build is that it has substantial forward firepower that also tracks right up to broadside ranges. The disadvantage is, for this firepower to be at it's best you want to be inside of 5km - and your tail is pretty vulnerable, having only 3 turrets available for defense.
You can go all-turrets as well though (6 and 2 torps, or 8 turrets) - the chief difference being sustained DPS (since there's no 'safe' arc against a turret boat) vs burst DPS (the cannon and turret boat hurts more if you're in the front 180 degree arc.)
I favor the cannon and turret set up since it makes me keep my nose on the target and again keeps my torpedoes aimed where I want them most of the time.
Those are the typical cruiser builds I can think of.
Oh, before I forget: I had something I wanted to mention about power levels. You probably already know this, but it's one of those "Just in case" things...
In most circumstances, keeping weapons at 100 power (plus whatever bonuses you have), is the way to go. You'll also want to check out
this episode of STOked - specifically the math segment. The key thing there is he talks about the Efficiency attribute; and it'll help you decide if you want to invest towards it or not, and in which skills if you do.
3) That's very similar to my own set up actually. Honestly it's worked fine for me; I think you're probably fine Boffwise, just do some testing and make sure you have them set up in a way that makes you comfortable. You can always get plenty more merits if you need to change skills out later.
If I had one "You cannot go wrong with this" suggestion, it'd be to give the tacoffs at least 1 Photon Grenade each of the maximum rank you can get them. Grenades in S4 are quite good, and having Boffs tossing them alongside you is well... nice! That said all the skills are useful so the big thing is getting comfortable.
4) Honestly you're really in luck here - STO on normal is *very* forgiving. It's harder in S4 on the ground than it used to be (the key thing being to pay attention due to everything moving so fast) - but all told it's hard to build something so bad it won't work.
So yeah, the main advice I can reiterate here is: Find something you're comfortable with. When you find something that suits you, it'll become second nature; which will cut out a lot of the danger from things moving too fast.
That said! I want to note I am not an expert on PVP. I do it from time to time... but mainly as a Klingon Sci officer in a carrier. >.< So my PVP advice is probably not very relevant unfortunately.
I'll have to leave that to someone else I'm afraid.
(I'll also add my warning label from my guide thread: Everything here is accurate as of my knowledge and has worked for me personally; but I make no guarantees >.> I find a lot of things in this game are YMMV; which is why I keep mentioning testing things out and finding what's comfortable.)
Oh, also, I don't know if you know, but you got a free respec with Season 4 - so that could help you out too.
And you're very welcome <^_^>b