thanks for all the replies.
The engine vibrates at idle to like 1500rpm, I am working to get the tach in to check the rpms. I think the idle rpms are low, and could suggest incorrect IP timing.
They do rock around a lot at the normal idle speed of 650-700rpm, I bumped mine up to maybe 800rpm which smooths it out a lot. Above 1000rpm they're very smooth and sweet for a large 4cyl diesel.
I would definitely check the injection timing.