1. I got along just fine in the past without these new-fangled mark II harvesters and econ stations. I would probably avoid those altogether and go for better fleet or starships instead, the return isn't all that great on your knowledge investment.
2. Unless there's an orbital mass driver or something equally starship-shattering, I generally send a full cap of all marks of raid starships to take out important targets, while my fleet camps out on my side of the wormhole. Raid starships decimate most guard posts, eyes and other individual targets pretty quickly, so you can be in and out pretty quick. It's even better to bring them in a transport or something so they don't have to run a gauntlet on the way in and out. If you need extra firepower, bomber starships are also reasonably fast and are good at zapping single targets.
In the latest beta versions, the ships released by your raids don't make a beeline for your worlds any more, but instead hang out in the back somewhere until you either leave yourself open to counterattack somewhere, or jump in when a wave or whatever comes in or they reach critical mass, so keep that in mind.
Superfortresses are one of those things that I tend to just avoid like the plague unless the world is absolutely critical.
3. Yeah. Unless there's an overriding reason to do so (like a golem or some other non-stupid capturable), don't take over planets with counter attack wave guard posts. If it's a neighbor, just neuter the system (destroy as many guard posts as you can, plus any warp gates or warp-gate-like structures) then get out.