I'll try to answer your questions in one post, it might get kinda long. Here goes:
I'm not a mechanic but pretty mechanically inclined having rebuilt several car and motorcycle engines in a previous life.... Also Selkie is the third "project" boat I have owned, however I think she will be a keeper.
Engine came as part of a "project" boat. Salt water had entered the crankcase after failure of shaft seals on raw water pump, which went unnoticed or ignored by PO until engine quit. Lots of surface rust on internals of engine. Raw water pump is on same shaft as the governor and the fuel injection pump, all of these were toast, as were the governor shaft bearings. Cylinder head was missing, as in I did not get one with engine.
I picked up a used cylinder head in fair condition, but after some attempts to get the engine to run (it did run, but poorly), I decided to tear the engine completely down and replace or restore every worn component, unless I came across something that forced me to condemn the entire engine.
The single most important thing in the entire project was finding an automotive machine shop and machine shop manager/head machinist that I could both trust and work with. I did this by taking the recommendations of the local Kubota dealer's mechanic, along with other recommendations from a couple of ex-mechanics I happen to know nearby. I also bought most of my parts through the local Kubota dealer, but also bought some from online sources. I used Kubota OE parts whenever available.
Basically I did all the dis-assembly and re-assembly work. I stripped the block down to the last nut and bolt, but did not touch the transmission besides changing the fluid in it. I also did all the parts sourcing and ordering. I did not find a rebuild 'kit', everything had to be order part by part.
I removed the motor from the boat using our marina's hand operated mast crane, and made a wooden dolly to transport and work on the engine. The work given to the machine shop included - measuring of component dimensions to determine if they needed replacement; the rebuilding of the alternator and starter; cleaning/de-greasing and paint removal from engine; and all the machining work described below.
So here's a list of what I replaced with new components:
cylinder sleeves, pistons and rings.
cylinder head valves, valve seats, valve guides, valve seals.
pushrods and tappets.
rod bearings, wrist pin bearings, crankshaft main and thrust bearings.
governor internals (balls, circlips, cone, sleeves etc).
governor shaft bearings.
fuel injection pump, fuel injectors.
raw water pump (changed to oberdorfer from sherwood).
all internal seals and gaskets.
Here is what the machine shop did:
-cleaned inside and outside of all components, stripped paint and sandblasted corrosion off as needed.
-measuring of component dimensions to determine what work should be done
-pressed out old cylinder sleeves and pressed in and re-bored new ones
-skimmed cylinder head face and cylinder block deck
-cut out and replaced valve seats to restore proper valve clearance (critical for good compression)
- removed and replaced valve guides; lapped in new valves and reassembled head with new valve seals
- ground crankshaft journals to correct dimension for new (oversize) bearings
-inspect and polish camshaft journals
- pressed in bearings and seals as needed
-removed and replaced all block plugs, thoroughly cleaned oil and coolant passageways.
-rebuilt OE alternator (including new bearings, brushes and regulator)
-rebuilt OE starter (including new bearings, brushes and solenoid)
Machine shop bill: $720 (I was surprised that it was not more)
Rebuild starter and alternator: $150
Biggest ticket Components:
Fuel injection pump: $300
Injectors: $200 (for two)
Raw water pump: $240
Engine mounts: $140 (for 3)
All other parts total: $700 (approx)
Special tools: $40 (oversize deep socket and adapter)
Total cost: $2490.
Although not included here, I also made a new engine panel with all new switches, gauges and senders (oil pressure, volts, water temp, rpm). The cost of this is not included above.
I have a few photos of the dis-assembly and re-assembly, they are not very informative but I can post them if anyone is interested.
Hope this helps, contact me for more info or questions I'm boud to have forgotten something