A couple of other thoughts...
In a sense, I don't think I really responded to your specific question about the Kubota engine, so I thought I would add a couple of notes.First, your idea about taking a Kubota engine of the same model number and coupling it to a Hurst transmission may have some merit on the face of it and, yes, it would appear to be cost-effective. There may be some hidden issues, i.e., footprint, spacing of the mounts, whether it actually fits the existing bed, whether the oil pump pick-up can run at a angle etc., that you have to take a serious look at or you could find yourself in the unenviable and expensive situation of having to do some re-engineering.Also, Steve Dion is right in his suggestion about finding a used Westerbeke. That would be a smarter option to explore than the Kubota per se. I don't know for sure, but I feel comfortable in saying that Westerbeke did not model itself after Kubota. It might be the other way around. And, with a used Westerbeke, you are buying a well-known and well-support "family" name. However, you may very well find that a used Westerbeke, again not necessarily with a warranty, will run you up to 2/3rds what a new one will. The Bukh engine, just for comparison, costs about $5k brand new and in the crate and comes with a great warranty and excellent support.Also, if you do nothing else as you embark on this project, make absolutely certain all your agreements are in writing. DO NOT fail in this! Make sure you have documents that say "Qoute" NOT "Estimate." Be sure you accept all QUOTES in writing and that you make clear that there will be NO change orders increasing the cost of the project without your specific written acceptance and agreement. Costs on a project like this, otherwise, can spiral quickly out of control. And, whatever your final number comes up to be, set aside about 20% for unexpected contigencies like maybe having to replace a fuel tank, replacing all your old fuel lines with new, replacing all your fuel/water separators or having to buy new ones, new control cables for the new engine and so on.Ok, enough. I'm off the soap box. Ask me questions if you have them and have great luck with your project.