Well what you're asking is a really tough question to answer. One because you are talking about modifying a previous system outside of its original design. But on that note, I think as long as you are taking the fuel from the bottom of the tank and filtering it you shouldn't have any problems. However be careful because the pump may still need to be in its up-right position to pump properly depending on the pump style. If it is a positive displacement pump as it should be though, there should be 0 issues in my opinion.
2005 Ski-Doo 600 H.O.