On the note of the "building the "ship" in sections and tugging it out there. Thats actually not unheard of in the forums here. Think there there was 1 guy who was doing "modular" ship designs before.
But getting tractor systems to work can be a bit of an orginizational nightmare.
Basically though there are 2 ways to do this.
1. Civilian engine>Military hardware section.
In this manner you can build abnormally large Civilian engine sections that won't eat up any MSP on the long voyage or need rampant naval yard expansion. Also a bit more efficient than military engines.
Coupled with a few Engine>Fuel tank ships to act as tankers and you can get a pretty long endurance fleet. Nice thing, if 1 of the engine sections does get damaged in combat, you can switch it out with 1 off of a tanker.
2. Also possible is bringing an Engine>hanger. And store a more proper warship in the hanger section (so you don't have to worry as much about maintenance), OR bring a military engine section in the hanger, to be switched out with the civilian one when you get into combat distance of the target.
3. Drop tanks. Rather than building a civilian engine and specialized military sections. Just keep your existing warships, but build some fuel/MSP/tractor sections that can be tractored onto them for the duration of the trip. Added bonus for this method is that when getting into combat range, you just unequip the tanks, and your ships will be right at normal combat speed.
I've actually done this one before with some cruisers (cruiser to me is a ship with long endurance to hang around away from bases for long periods) to moderate degrees of sucess, helpful also that when the tanks were dropped by the ships in question, they ended up being bait for some enemy fire while my ships sped away.
Personally for your particular mission profile, 2 would be my tactic. A hanger section to house any given ship is generally 5-20% bigger as far as the hangers go. A bit of space is wasted in crew quarters, a magazine for reloads if you're using box launchers, and any other extracurriculars. But guessing that to tote around a 30kt ship, you're probably looking at a ~40kt section, which can be hauled by a 120kt engine section (~50% engine, ~50% fuel) probably wouldn't be too far off. Bonus points, when you get there, you'll have hangers for your fleet so you don't have to worry about maintenance for a while longer, because on extremely long deployments, the maint can kill you.
Also a standard hanger section can work for any kind of ship, be it a sensor scout, a battleship, or a few dozen FACs or fighters.
Anything that can be made 100% civilian though should be, because of how fast you can modify civvy shipyards.
But how you do it is up to you.
Couple things I wonder about though. Whats the orbital speed of the target planets, or the stars they are around, around the central star in the system.
You might find that it'd be a lot more efficient, to do some math, figure out how long it would take to get to the target destination. Figure out about how much farther along its orbit it will be, and head towards where the planet will be, rather than just a simple "move to" which you may find spends a lot of extra time and fuel curving along to the area.