I have managed to sort this by copying the default Warthog bindings, renaming (incl line 2) and it now works fine, pedals and all key assignments are now saved (although) I did have to add the key bindings in the options screen, I couldn't see any default key assignments in the default Warthog file.
Anywayup, it now looks like I have cracked it.... {touch wood}
EDIT - no matter how solid and capable this felt, I just found it too awkward to get used to. So saved myself £280 I suppose.
If anyone is interested in the bindings, here they are at mcdee:
https://www.mcdee.net/elite/binds/ejebyk