The Main difficulty would be the HUD. You would have to choose between the pl HUD and the ctf HUD. If you choose pl HUD, not enough info for RED and ctf HUD doesn't give enough info for BLU.
However if you do choose one of these HUDs are adequate, making the "cargo" would be as easy as parenting the intel to the cart, then you just build the payload and flag game mechanics separately, (provided the is only one win outcome for each team, you probably don't want RED to win by time or caps) or copy them from boojum's library and edit it.