Hey SKTP, wow, didn't mean to leave you hanging. I'm betting your tranny is back in business but I'm no where near the point of reassembly. So I basically don't know the answer. I would think just for wear sake, they should go back the way the came. What did you end up doing?
My cases are getting sonic washed this week so I'm thinking about the cylinders. One of them has what look likes surface rust but you can't feel a thing when you run your fingers over it. I'm hoping I can, at the most, just re-ring the pistons and not do anything to the cylinders. Maybe even use the old rings. As you can see in the picture, the cross hatching is still visible from the factory so I'm thinking very little wear. What do you think?
There's actually quite a bit of wear showing there: when you can see where the rings reverse direction like in the top picture, it's worn. You can take a hone with long stones (3" long) and run it for a minute or two (with light oil) and then it will highlight all the worn areas for you. Be sure to constantly move the hone up & down in the bore as you do so you don't wear it in just one place.
Once you've done this surface honing, and can see where the most wear is happening (which will be the top ring's spot), you continue to hone until the whole cylinder is even and no more of these marks are visible. Then wash the bore clean, remove the piston's rings, and insert it upside-down into the bore until the end of the skirt is perched at the point where the top ring used to be outlined in the bore. The piston must be aligned as it it had the wrist pin in the rod, so the widest part of the skirt is toward the front and back of the engine. This is the point where you want to now measure the bore wear by sliding feeler gages in between the bore and the skirt at the end of the skirt, by lifting the piston skirt up out of the bore, sliding the gage in with it and pushing it down to the wear spot, then try to pull it out. If it comes out easily, go up one size on the feeler gage and repeat. When it finally traps the feeler gage, the clearance may be considered to be one thickness less than the 'stuck' one.
If you have more accurate ID bore gages, it is far easier to measure the wear at the ring site, though. You just put them in at the site, then measure the gage with a micrometer. (All these steps are shwon in my book, for the novice.
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