Usually the JD liners are not that difficult to remove. Come from underneath with a good solid piece of wood (like a slug hammer handle). Going on either side of the crank you can catch the bottom edge of the liner, usually a few good hits with a heavy hammer will drive it up enough that you can get a pry bar under the lip from the top side and pull it out (sometimes you can just lift them out by hand). All you need to do is move it up an inch or two and it's free. I have had a few stubborn one's that would split the end of the wooden handle so I use the flat end of a long steel punch/bar, just be careful and don't let it jump off and damage one of the main journals. It would be good idea to wrap both it and the journal with some sort of protection.
Also, be careful when turning the engine over while installing the pistons/rods. Sometimes a piston will try and push a freshly installed (soaped) liner back out. You can use a large flat washer to catch the edge of the liner and use a short bolt in one of the head bolt holes to stop this from happening but with only two liners to install, you can probably just watch it close.
Make sure you use some water conditioner to prevent this from happening again. CCSIAL mentioned a Fleetguard product and JD has their own version. I'm sure either is fine.