I see that the YS-03 is Slave TTL-only: it has no manual control or power adjustment.
While you mention you are shooting in manual exposure mode, what camera flash mode are you using: auto, fill, manual, etc? Also - what metering mode are you using (spot, center, matrix, etc)?
Shooting the camera in manual mode, while the flash is in TTL mode, can lead to under or over exposure depending on the above settings.
I don't use this strobe, Sony cameras or TTL , but for starters I would test the TTL set up. In a dark room with a test subject set camera to A, S or P mode, set camera flash mode to 'Fill' and play with exposure and flash compensation settings as required. Try with or without the focus flight. See if you can get decent shots that way first.
With Manual exposure and TTL flash you set a manual exposure to get the background lighting. The strobe then completely ignores this and fires until the camera determines that the metering area averages mid grey. Being a strobe this will be your foreground being lit up. This is ok if the subject fills the metering area. Its less ok if the metering area is a small critter with a water or distant background: the strobe will overexposure the critter and foreground until the entire metering area averages a mid-grey exposure. In such cases test spot metering in a dark room with a small subject and an empty background, and be prepared to use the flash compensation setting to dial flash exposure down a stop or two.
On focus lights and it being too dark to focus - I use a small 1000 lumen focus light with strobe auto off, usually at half power (500 lumens) without any issues. What helps here is setting my screen to always be bright regardless of exposure settings (ie turn off exposure preview). I can see the shot, and if its in focus, even when manual shooting night dives. I'm sure Sony has this feature somewhere in its set up [EDIT: Turn off 'Live View Display' in one of the camera settings sub menus]
Cheers
Rohan.