For the nozzle soak/wash you "should" have a cleaning cartridge in the back slot for that (I have always just refilled ours with regular cleaning solution with zero problem). Anyways when you first go in it moves the wiper and gives you an opportunity to clean the wiper, then press enter, on the next screen when it says "fill the liquid" you are supposed to press the function key and it will dispense a small amount of solution from the cleaning cartridge. You can press it multiple times to fill the cap. I think many people are not aware of this.... then enter, then set the amount of time to soak.
Anyways multiple things can cause these problems. Dampers, pump, capping top, capping top alignment, any sort of air leak anywhere, partially clogged tubing, etc. One thing I have run into literally many times over the years with both the old JV3 we had and our JV33 is using generic (cheap Chinese) aftermarket parts. Not all are bad by any means but I can show you pictures of multiple bad generic pumps that fail in many ways from their tubing splitting open in them, falling apart, to just not really pumping much through. Most recently pictures of defective cheap dampers and a cheap capping top.... the dampers for all intents and purposes looked just fine and dandy and for $5 or so each that's great. Except for after much hair pulling and troubleshooting I finally did some pressure testing of one not in the machine using a syringe and discovered that there were pinhole leaks in the plastic near the bottom nipple. Literally cannot see it with your naked eye but on putting a tiny bit of pressure ink squirted out! In use it was just the opposite - it would draw air in. New capping top that the top rubber edge was just not consistent and would also cause leaks.
Over the past 10+ years this is one thing I have learned over and over again. Every time I try to cheap out and use certain generic parts it always bites me in the a$$. Dampers, pumps, and capping tops specifically. Some thing like tubing and wipers, no problem, I'll use whatever is cheap. For some odd reason a genuine OEM Mimaki pump lasts 3+ years while not a single (and I've tried over a dozen over the years) cheaper aftermarket pump has lasted more than 6 months. Just saying to keep this in mind. You may well have used all OEM parts but if not, some cheap parts might very well be part of the problems. I've also seen another member post here in the past 6 months or so who bought a used/floor/demo (cannot remember which) from an official authorized Mimaki dealer. That dealer told them they put in a new pump and some other new parts. They had problems and posted here about it. As soon as they posted a picture under the capping station it was immediately obvious that the dealer did not even use a genuine Mimaki pump (it has white tubing!! lol). They called them out on it and the dealer came clean and admitted it and got them a new OEM pump....