With all the symptoms you have posted over the last month, you may very well be at that rebuild vs. new question. Unless you are an experienced diesel mechanic, I wouldn't recommend trying to rebuild it youself. When I had mine rebuilt this summer, the parts were about three times the labor cost, and did not include a new crank crank ($900) or connecting rods.
For the record a re-manufactured engine from Mack boring is about $5200 + freight & installation; I believe a new engine is north of $10,000. Any Yamnar dealer can give you a quote on both options.
If you want more detail contact me thru the IP homeport site