If you have the off-center bolt on either the flex plate or the torque converter marked - then there are 4 possibilities. But if neither is marked and all you can see through the opening is one flex plate and one torque converter hole each at a time - you can rotate the converter through all 4 positions on the first flex plate bolt and never know if you find a match because you can't see all the holes at once. You can then rotate the flex plate to bring the next hole into view and again rotate the converter through all four positions trying to find a match for one where all the other holes line up - but you really never know because you can't see all four holes in each at once. 4 x 4 = 16 possibilities but it's actually worse than that because unless you get real lucky you may not know when you hit the right alignment because you can't see all the bolt holes and their alignment at one time. It's enough to drive you crazy.
Short of pulling the transmission again here is what I would do, rotate and mark the 4 torque converter holes 1, 2, 3 and 4. Carefully measure center to center for each set of holes and record the dimensions until you identify the off-center hole. You aren't dealing with a major difference - 1/4 inch or less I think, so have to measure carefully. Turn the torque converter and try to get the off-set hole and an adjacent hole both in view at the same time though the splash shield opening. Then rotate the engine and flex plate until you get a match to those two holes and slip the two bolts in loosely. Then turn the engine and insert the other two bolts - I can't see any way this should not work as long as you can see two bolts at once.