I agree with most of the observations. The stretch for me right now is that I lack mobile maintenance bays and asteroid mining modules. So, it was trying to find a way to address maintenance outside of using those items till I get the research in. Doesn't help that I lack a scientist with that specialization.
The challenge is running into an active multi-system hostile so early. I have run into hostile NPR's a jump or two away before, but managed to win the naval engagement, then invade their homeworlds and acquire maintenance facilities that way. This situation is much more like the WWII island hopping campaign. I know the NPR empire stretches out further than I have explored, and I don't have a method to drop instant forward bases like I did in previous games where I had more developed tech and infrastructure.
So far, the lesson for the future start up games is to start looking at some picket fleets with larger maintenance parts on board, but that's really only a stop gap. Stopping the overhaul clock is really the kicker, since it keeps the fleets "in service" longer by eliminating the frequent overhauls required right now.
I have run ships for quite some time by just refilling spares, and then discovered the nasty tendency for ships that have run that long without overhaul to spontaneously explode.
As far as the actual system defense, in previous games after taking the system I usually mine and drop sensor buoys on all the warp points, then move a mobile force in system with fleet support. If its expected to be a really hot system, I usually have a dedicated jump point defense squadron that's beam armed and armored to the teeth sitting on the jump point. In key systems, they get backed up with heavy beam defense bases backed up with missile and fighter bases staggered out away from the jump point. I have found a couple of squadrons of gauss armed fighter squadrons on CAP right on the point makes a big difference on the initial incursion.
I also had good luck in a previous game setting up long range/long endurance FAC tenders with a squadron or two of FAC's as forward fire breaks to bloody up enemy ships transiting into contested systems.