The LI upgrade is a very good idea since it can help prevent acid damage to your boards in the long run, but it shouldn't be necessary for your boardset to work correctly. Those AA battery holders are kinda flimsy, and since you have been changing the batteries on a regular schedule (kudos, BTW, not everyone does that!), they may need a little maintenance.
Since you were able to fix your other problems by cleaning up the interface board, you are on the right track by doing the same with the battery holders. You might also want to check the solder joints on the battery holders, too, may they have loosened up a bit from the regular battery changes. If you use a 20-30W soldering iron, you should be able to reflow the solder joints easily without damaging your CPU board, but still use caution and don't leave the iron on the traces too long or you could cause them to lift off the board.