Mine was busted due to some thick paper and a head strike. Service was as much as the thing costs new (Epson parts are insanely priced, like a new print head alone out of China costs more than the 3880 new with rebates!) so I tore into it figuring nothing to lose. Lots of thin flimsy plastic panels surround the innards and why they put so much blue "assembly & shipping" tape on it too. Half the battle is getting the outsides off, and the ink cart unit (Ink cart holder unit, hoses, dampner, ink switcher, are a single repair piece. $150 or so?).
I got as deep into it as pulling the entire print head and carriage it sits in out, along with all the ink lines. Had the capping station out to as the print head and carriage slides off the rail to the right side. When I got into the splitting the head from the dampner unit and switch-over MK/PK thing, I dribbled some head cleaner into all the upright ports in the dampner and wiped off the gasket around each one that seals to the ink supply line. Fwiw, there was a lot of plastic shards and crude on the gaskets around each nozzle left from the factory so maybe air leaks could happen there. Just took a lot of photos and three pages of notes. Mostly all Phillips head screws, and a long pair of stout tweezers to do it all.
Never got into that 2manuals software. Seems like it was pirated in that the computer date needs to go back several years, and maybe it is made for Windows XP and the 3800 too. I think there is separate ones for the 3800 and 3880 so maybe the communication problem is that.
There was someone who had some color targets that were specific to each tank, sort of a cleaning or checking deal. I think Qimage Ultimate also can do individual ink colors, or all at once, in some sort of pulsing mode. Any time mine has plugged bad, it takes more than two 'power' cleaning cycles and then letting it sit for a day before it begins flowing again. Seems more so when a nozzle plugs or loses a line, I do a 'minor' cleaning, and checking again and another plugs along with maybe the first one. Odd. So a couple of 'power' cleans and sitting overnight usually brings it back online the next day.
That capping station has a couple of clear silicon drain hoses under it. They wind to the motor that moves the wiper blade and raises and lowers the capping station unit, but I suspect whatever it does is just to clear the drain lines as it holds ink in them to seal off the air from the maintenance tank drain, somewhat like an air lock. No vacuum there as it isn't that well sealed nor that much of a sealed motor either. I think the entire ink delivery is off that bellows air pump in the left side and it doesn't seem like much pressure. Too bad it isn't measurable somewhere (Software?), but still a major drop would affect all tanks I think and not just one.
Have you tried an OEM ink tank to see? Couldn't hurt. Maybe a leak on the inlet pressure side of the cart or in the printer's ink drawer.