What's the first thing you do after getting water ran to your new piece of property? Give the old girl thanks for doing so.
I immediately pissed on it to re-establish dominance and gave it a good greasing.
If you have the backhoe on when parking in the container, leave the hoe up until the rear tires are in the door and then lower. It will get a little light on the front end if you lower before going in.
Then, don't forget to lower once in!
OP, I'd machine that flywheel in a heart beat and never think twice. If you take it to a good machine shop, they'll likely also have spacers you'd add between the crank and flywheel that is the thickness of the material removed.
A friend of mine has the double (quad) forks on a skid of his. He runs a small junk yard and uses the extra forks to enable him to lift more while still using relatively small forks.