Well it turns out I was being a bit of a twit, I accidently saved the original file as half it's size after doing the byteswap so when I burned the EPROMs they were only half full.
I now have a working Iron Solder cart. Thanks for your help folks.
So to recap, all I did was byteswap the rom file, then dissect it by word using winhex and then write those to two 27c800 eproms. The first file spit out from winhex being the high words, the second being the low (top rom, bottom rom on the cart).
For those interested, both mask roms were faulty. Several bits were incorrect on both when comparing them to the roms I found online and ultimately used.