I'll say it one more time.
You are very unlikely to get a stable world by taking the world files from the world you just made, and putting them in a new copy of mindcrack or direwolf. This is not a reasonable thing to attempt. The sort of requirement in scripting to convert the old item numbers to new represent far more hours of work then most sane people would be willing to spend.
You can either get the hopes of your players up, and then disappoint them, or have them strip down to vanilla resources and ores, write down the net worth of each player, and then award it back to them on the new server. X stacks of iron, Y stacks of diamond, Z stacks of tin... each person restricted to a single 17 slot inventory, no tools, no armor, no enchantments and turn them loose with the bonus supplies in a new world.
I know this sounds crewel, but you are not carefully nursing a server from 1.2.5 through all the patches, one small change at a time. You are not making small changes and translations. You are talking about months of changes all in one hammerblow.