MasterMike. I find that utilizing the parts books to ID parts, then reverse engineering the other applications it is used in is the best way to find answers. The one site sponsor has some Kioti Parts books online.
Parts Finder Michigan Iron & Equipment Morrice, MI (855) 265-459?
Looking at the DK45SE engine block I see it is a parent bore engine aka sleeveless. This means you would have to have a machine shop hone it out and put in oversized pistons if they are even available, which they are not. You might be able to have a custom repair sleeve made, have the block bored out, and then reassemble, but if the water passages are too close you could end up with an worthless block and lots of machine shop time.
So we are stuck finding a new engine. There are three cylinder block assemblies used with this engine, however it appears that they all have been superseded by E6340-A0012.
Your crankshaft will also need to be examined and turned down if scratched, however it appears Kioti does not offer undersized rod and main bearings, so you would have to get a new crank.
Remember, you will need a new block, pistons, piston rings, New piston pin bushings, main and rod bearings, gaskets for everything mounted to the block. Due to oil starvation / metal contamination a new oil pump is a good idea too. Your cost for just the block is about to double if you do the work yourself. If you hire the work out it might not be economically feasible, compared to replacement cost of the machine.
What does the tag on the engine say it is? Worst case scenario there are some DK45 at salvage yards and it might be worth looking into to see if a DK45 engine will fit in a DK45SE.
Kioti Salvage
There are some rumblings on the internet about the Daedong 4A220 being the same as the Kubota V2203 and might be worth investigating.