Nicholas, first of all why do you think the engine needs rebuilt...what is wrong with it? I have rebuilt a few engines in my day, and I have had a few people ask me to rebuild engines for them and come to find out there was no need to rebuild. I have had to remove and rebuild heads and have had a couple times bad diesel injectors made engine run so rough they thought the engine was about to blow.
If the engine really needs rebuilt and you don't want to tackle it, like Keith said, call around and see if another mechanic at another course may want to do it on the side. I have rebuilt a couple Yanmar engines and they are pretty easy to rebuild, but one I came across had damage to the block where the crankshaft bearings and shims gave way and the crankshaft slid back and forth hitting the block. In this case, the block was damaged and had to be replaced. Likely on Yanmar engine, if you have the engine out and you can grab the crankshaft and it slides back and forth the slightest amount, good chance the block will have to be replaced...not defenite, but good chance.
Where are you located? I would recommend go online with Yanmar and find a local dealer and service center and get a price from them, or call your local Deere dealer and see if they don't happen to have a 3245C they are parting out and have an engine. I know a used equipment dealer I will ask if he knows of any engines around, but you could also call used equipment dealers and see what they have, you may even try Cutter Equipment in Canton, Ohio
http://www.cutteronline.comPaul L Double