Kevin,
Okay on the labeling and that you are using the right part for the right side. Also, your orientation looks correct.
Here is what I see. The picture where you show the tape measure, the bottom part (below the tape in the picture) goes from the rocker flange to the bottom of the frame rail laid up to the rail from underneath, so not sure why that part would be deemed as not fitting since one side butts up (R) and the other lays up (L). On the vertical portion (above the tape in the picture) the left side butts up to the frame rail and the right side lays over the end of the front flange of the end of the rocker. Again, I do not see where this would be deemed as not fitting. Perhaps the end of the pieces look obviously out of place and thus your observations, but they do not butt on both sides in either case so theoretically you should be able to put the piece in and trim accordingly (not saying you should do this). Having said that, if the left side fits correctly and measurements on that side show that the new will fit properly in place of the old, that is a good sign. Do the measurements match between both of the replacement pieces (L & R)? Was there any evidence of damage on the TB you removed (crushed at all side to side) that would support the notion of the rocker being pushed inward? Do measurements L and R (of the car) suggest that the right side TB space is narrower than the left? The answer lays somewhere in the sorts of questions I am asking, detective work is called for (and should still be possible with where you are in the process).
BTW, please note the missing stubs on the inboard side (toward frame rail) of the tops (where your feet land) of the TB's. You need to either need to take the corresponding pieces from the original TB's or to make new pieces and append them to the new TB's once installed. See my ECI thread for more/pictures on this (early, in the first few pages). There is a flange on the frame rails that end facing where the toeboard sheet metal goes which the TB should lay up to. The way they are cut, the TB ends before it reaches the frame rail flange.
Also (and finally), please do take Tom up on his offer (call him) if my posts are not getting you going in the right direction. Tom is very helpful (and willing to help) and was a big help to me as I went through the process. On the other hand, I will help you however I can, just let me know what other questions you have and/or what doesn't make sense in what I have posted.
Good luck and regards,
Bob
