I did an inframe on my 3000D 10 years ago. Usually the lower end on a diesel is what's worn out first. If let go long enough then the top goes too. My Ford had a different problem. The PO's operators removed the air filter hose to the intake manifold and operated the tractor in a very bad environment. The top end was so bad that you needed ether to start it in the summer in N. TX.....my first diesel purchase and I didn't know why one needs ether in the summer to start a diesel...but I know now. Grin
I went to the Ford dealer and asked who did machine work for them and was told of a machine shop close enough. I went to them with the head and not only did they do the head but sold me new pistons and rings plus inserts (bearings) for the rod to crankshaft interface.
Getting to the bottom is no biggie. Just drain the oil and unbolt it. Don't remember but you may need to undo the bolt holding the oil pump pickup screen to get it out and out of the way to get to all of the rod bolts once you drop the "pan". Nothing magic about them. Once you unbolt them and you pull the caps off, with the head off you just push them up and out of the cylinder. No sleeves on these engines which is great for me anyway. When you pull the caps off the rods pay attention to the "sleeves" under the caps and rods. These are your bearings and are to be replaced.....called "inserts".
Most times there is a ridge cut into the top of the cylinder where the upper ring stops moving up. Auto parts stores sell a tool that cuts that ridge out, may rent one, so that you can push the piston out. Just cut enough to get the piston out.
I checked a couple of mains and they were ok so I only replaced the rod bearings (inserts). Had I needed to replace the mains I would have had to pull the engine and I really didn't want to do all that working alone and all.
I measured the cylinders with a new ring (see next paragraph for how to do it) and they were close enough to not have to pull the engine and have it bored. I did put the cross hatch hone pattern on to cut the glaze on the cylinder walls so that the new rings will "seat"....wear in to fit the cylinder.
Go to your Ford dealer and get an after market repair manual. I don't have them in front of me (out in the shop) and it's cool and raining here today....N. TX. July 31 and it's cool and raining....whadda deal. I think the name is I&T and the number is somewhere around 40 or 41 as I recall. Tractor covered is on the front cover. Cost is about $25 and has all I needed to get her apart and back together.......I just googled "I and T manuals for Ford 4000" and found lots of entries. Seems Amazon has them too. You need them for torque specks if nothing else.
So if you have ever been into an engine and are mechanically inclined go for it. As I said I did mine about 10 years ago, didn't go back and tweak the valves or anything.....used Kopper Koat gasket coating for the head gasket, the engine is diesel with the associated high compression and have had zero problems. I guess I got it right.
HTH,
Mark