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Thanks to some information TrackStar gave me along with some help from Schoolloans, I was able to find a lower rear ball joint solution. Apparently, the front lower ball joint from a 1997 Honda Accord is the same as the rear lower from the S2000. I found it easier to have a local shop press the old ball joint out. The tool of choice was one of those C-clamp tools with a well placed adapter sleeve, then an air chisel under the lip to finish the removal. The new one was pressed in by first putting the ball joint in the freezer, then installing it with a homemade C-clamp rig. Here is the picture of the replacement ball joint next to OEM:
One on the right is the new replacement ball joint. The one on the left is the OEM one without the rubber boot.
Go to any decent parts supplier (NAPA or the supplier to your local mechanics) and give them the MOOG part #K9643. Unless you have the right ball joint press adapter, I'd recommend taking the knuckle to a mechanic who does and have them remove the old one. See above for how to replace with the new one.