Hey, wow ! I've never seen a cable operated clutch on a 505.
My understanding of the liner tool is that it makes them sit down as far as they will go. That way you can measure protrusion, as it is measured in thousandths of an inch. Unless you make them sit down, they may not have seated properly and you will get a false reading.
The tool will not make them stay down.
When you took out your liners, I'm sure they were stuck in place, but that was only because of corrosion and perhaps some gum (oil residue).
There is a very small gap between liners and the block. They are a close fit, but they will move around if, in the future, you take off the head. That is why people recommend using bolts or studs with large washers to hold down the liners. If they move when you have taken off the head, then you have got coolant and grit between the bottoms of the liners and the block. Then the bottoms will not seal properly.
If you want to avoid taking out the engine, just take off the cylinder head, and take off the sump.
Push out the pistons etc from the bottom. You will have to take off the oil pump again, but that's easy. Then lever out the liners (if you are going to take them out) with two large screwdrivers, moving back and forth.
It's all a bit of a strain on your back because you have to lean over the engine for a long time, but I've done it quite a few times.
If you're worried about the main bearings, just take off one or two bearing caps and examine the shells inside, then torque them up again. No problem.
P.S : Did you put in a new O-ring between the oil pump and the block ?