What smurphny said, PLUS parts for the Kubota engines are cheaper then most other engines (Volvo, Westerbeke, Universal). Volvo's probably have the worst reputation for hard to find and EXPENSIVE parts but all branded parts will be more $$$ then for a Kubota; so do yourself a favor and cross Volvo off your used diesel engine list.
The $7k price for a brand new Beta is what it is. There will be other costs associated with a diesel re-power job though: new fuel tank & lines, might as well re-do the hot section of the exhaust, cutless bearing and stuffing box while you are at it, and you might need a new prop and/or shaft coupling for whatever HP engine you end up with.
Use eBay and CL to hunt down used diesels in your area. I'd ask around at your local boat yards as well.
A re-power is not going to be cheap; cheaper if you can do most of it yourself though.
You might be able to get around ~$1K for an Atomic 4 in good working order on the used market.
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