Take this advice based on how much you've paid for it
Our Yanmar diesels (I also have a Hunter 34) don't have glow plugs so they will always be rather hard starting in cold weather.
I have been trying to track down the reason for the occasional rough start up. It's a random event which makes it difficult to pinpoint. I've tried to eliminate air leaks so I'm leaning toward a sticking injector possibility.
I'd recommend checking the compression on all cylinders and making sure valve timing is good.
Generally if compression and valve timing are good, it's a fuel delivery issue not a need for an engine overhaul.
As far as the engine jumping around as the throttle is advanced, I have the same problem (especially after the engine is up to temp). I've had the prop shaft checked, the prop balanced, new cutlass bearing, motor mounts removed and inspected, and had the overall alignment of the drive train adjusted. None of these has changed anything.
I still experience the "pounding" until rpm's advance beyond about 1500 after which the throttle can be backed off and the rpm's drop while the engine operates smoothly.
I'm pretty sure the pounding comes from the tranny. The recommended fix is to ensure the gear selector is fully engaging the selected gear. If this is the case, I'm thinking a tranny rebuild is in the future with replacement of the cone clutch.
I plan to live with the problem for a while to see if it gets worse (which it hasn't since I've owned the boat) now that I'm sure all the supporting stuff is fine.