This is the answer to my own question that I found with help from the author of the below two blog write ups that I was using together to create a two switch backbone that was connected via GRE over two gig ports to service a fully meshed frame relay network (works great if you have two smaller routers with room for only two T1's each, which gives you 4 connected frame relay routers for your lab). The problem that I didn't understand was the DLCI mapping portion.
Basic router layout:
R1 <- Serial -> FRSW1 <- GRE via Gig -> FRSW2 <- Serial -> R2
http://mikemstech.blogspot.com/2012/05/frame-relay-switching-lab-using.html
http://mikemstech.blogspot.com/2012/03/cisco-frame-relay-switching-lab-fully.html
The fix, or missing part:
One router uses normal DLCI route statements such as:
frame-relay route 105 interface Tunnel0 501 (this side does the translations for both directions of traffic)
The other side uses a different DLCI route statement such as:
frame-relay route 501 interface Tunnel0 501 (this pushes it through the tunnel to the other side as an untranslated DLCI)
R1 -> FRSW1 is one half, and R2 to FRSW2 through to FRSW1's tunnel is the other half.
Hope this helps someone out