Seems like you have a pretty good economy built up, so Im hoping cash is not a big deal for you. So you have 4 starbases each with 3 remaining upgrade slots eh? I would go with a variety of things. First, you would be wise to upgrade hp/shields/armor on them. This will give you some time if your enemies decide to bring in assault cruisers (which can take down SB very quickly). Most people will upgrade health to max, but since you have 4 starbases clusterd to gether you can probably get away with just 1 upgrade for each of them so long as you have researched TECs health, shields and armor upgrades from the military tech tree to as high as you can. You'll also want to research improved degradation from the defense tree, as well as unbreachable hull and advanced fire control. That will make it hurt their ships more if they want to leave the stars gravity well while theres still a starbase there, and increase the hull/armor and firepower of your sbs. I don't think you can extend trade chains from star to star, but Ive never tried it so I dont know for sure. I'd upgrade 1 with remote construction, so you can pump out some extra units if you get in trouble (especially hoshis, or flak, or even Ogrovs if you have to face down an Orkulus[not very likely]). Go with docking booms on 1 of them. Upgrade health as high as you can on 1 (to be your big badass SB). And on the starbase that is the LEAST likely to be attacked (or is the MOST LIKELY to be attacked LAST) do safety override protocol AKA Big Red Button(BRB). That way if the enemy somehow plows through three of your starbases, you can press the big red button and wipe out any of his non capital ships that are in range. You can still do this if that starbase is the first to be attacked, but you may accidentally damage the others ( they can take it and be ok, just better to not have to repair it) In summary I recommend:

SB1: Hangar/Hangar/Hangar/Weapons/Weapons/Health/Health/Health

SB2: Hangar/Hangar/Hangar/Weapons/Weapons/Health/Docking Booms/Docking Booms

SB3: Hangar/Hangar/Hangar/Weapons/Weapons/Health/Remote Construction/Remote Construction

SB4: Hangar/Hangar/Hangar/Weapons/Weapons/Health/BRB/BRB

It is actually necessary to have an SB with the Trade Port upgrade in Entrenchment/Diplomacy in order to make your longest trade route go through a star. In Vanilla Sins, trade routes automatically consider neutral gravity wells, but in Ent/Diplo, it only considers neutrals with an SB with the Trade upgrade.

This also has the effect of making Magnetic Clouds pretty much useless in Ent/Diplo.

Keep in mind, non of those SBS have health upgrades, so there about as tough as a low level cap ship. A couple of stray Ogrov torpedoes, and a handful of HC and bombers could mean bad news for 1 or 2 of them. Plus why let those perfectly good upgrade slots go to waste . Go ahead and make em impenetrable to 2000 fleet supply, so you don't even have to worry about it. If anything, the AI is known for being persistent. It may not be able to take on all 4 and win in one battle, but without adequate health and healing, it can eventually wear them down. Which is why I suggest at least 1 health upgrade for each, Docking booms, unbreachable hull tech and remote construction (for hoshis!) Better safe than sorry.

Thanks for the advice, guys.

I'm curious, how does the Docking Boom work? Does it apply in a certain radius or does it blanket the whole gravity well like what the Sova Carrier's Embargo + Rapid Manufacturing abilities do?

Also, can these Docking Booms stack up? Meaning if I have 4 Docking Booms, will they repair stuff crazy fast, well worth giving up 1 health upgrade?

To my recollection, docking booms doesnt stack. But thats what you get hoshikos for. Docking booms heals for 15 hp/s for 60 seconds, which isnt a whole lot, BUT if you add hoshikos on top of that you can heal more. Docking booms also restore AM on nearby units, so that added in with the stars AM regen bonus, mean your hoshis wont be running out of AM anytime soon. So set them to "attack local area only" and they'll weave in and out of your starbases, patching them up in between and during waves of enemies. A couple of cielo command cruisers may also be useful. They can cast designate target on enemy ships, increasing the damage you do to them by 40%. The idea here is your starbases combined firepower will eradicate anything that tries to attack them, and your docking booms and hoshis will keep them from getting worn down.