Yeah, IIRC they have to completely run down their maintenance clocks when you order overhauls. Could always SM-teleport them elsewhere, but I'm not sure what that might break. Remember that you have both crew and mechanical deployment times. Morale is recovered just by staying at a population center.
Madman, in terms of how I start my campaigns:
I'll ignore conventional, since those start with 50-150 years of turtling and up-teching for me.
Research: Spend my starting RP manually. Set my labs to priority research goals, mainly the next drive tech, industrial rate improvements, and better gauss + missiles.
Industry: Start queuing up industrial expansions as population allows. Automines > factories up to a round number (usually 500-1000) > labs > shipyard expansions. Everything else is secondary. Get one commercial yard large enough to build standard-hold freighters and their colony ship equivalents. Leapfrog another commercial yard past that to at least 100k tons for terraformers. Get one military yard into multiple slipways for disposable survey ships and FACs.
Exploration: Design and build small, cheap survey ships ASAP. One or two of each type without JDs to explore Sol. Once that's getting close to finished, make versions with JDs. Pop one JP at a time, using all jump-capable survey ships to explore it. If it's completely surveyed without contact, it's probably clear, but I don't assume until I can get either a hefty DSTS colony or a system-wide active sensor platform there. Proceed like this, exploring one system down each chain until all are totally surveyed or found to be inhabited. Split the survey ships into grav/geo pairs, one pair to each chain, start exploring a second jump down each chain. And so it goes. Isolate inhabited systems, build Sol-side JGs to allow down-chain travel, complete the flipside JGs once the system has been confirmed clear and colonized at/beyond.
Colonization: Once a system has been confirmed clear with sensors, drop a seed colony on any inhabitable world. Add infrastructure as needed, slap outdated ships in orbit to keep complaints down (or garrison battalions if none are available). Any useful mineral concentrations get some automines once Sol is being fully exploited. Back at Sol, terraformers should already be at work on the useful bodies, and if there are any gas giants with useful Sorium deposits the first harvesting bases should be rolling out.
Military: Cheap FACs with X/O rail missiles or the best available E/KW in sufficient quantities to quell unrest, build nothing more until threats are encountered. But keep teching and expanding shipyards. Once the first Precursors are encountered, estimate numbers and put together a small strike group of frigates capable of knocking them off with long-ranged missile fire, make sure you have a salvage group ready to follow up. Stay the fuck away from Swarm, Invaders, and NPRs for the time being.
Longer term, important goals are snowballing lab numbers: the better your industry and larger your population, the faster you can add more labs, which further increase both your industrial production and research production, making it easier to further add labs. This is your biggest advantage over NPRs, you can macro like crazy. Also, continual shipyard expansion whenever you can afford it. Having lots of slipways and large slipways plus high industrial production rates means that you can very easily design and build new ships for new threats. This is why I don't build much military early: if you're found you're probably fucked either way, and it draws time and resources away from booming your economy, where all-inning on your macro game gets you to the point where you can churn out effective military units sooner. If you have low resources in Sol early military is also largely a waste of minerals: most of it won't get used and will be wasted if it is.
Incidentally, that ability to tech and industry-boom is why I like to start with 500%+ difficulty NPRs (with 0% encounter chance for other NPRs and a lower ~10-20% encounter chance for me), so that they are building up at the same time and will present a larger challenge. I usually turn the difficulty higher after getting built up so that any new ones spawned by my exploration will at least have numerical superiority. Low-difficulty high-rate is dull because you have to xenocide them off half the inhabitable worlds but they're not actually dangerous at all.