Spray foam is great for filling mouse holes.
Is the leak current or old? Where is the furnace located? We have had water around/under our furnace twice: fridge drain line (on right of furnace) and a hot water fitting was dripping under our sink (on left of furnace). Neither were in the sub-floor or the furnace, that is just where the water ended up.
The fill neck can be patched if it is gravity fed. Our gravity fill is near our furnace and water sloshing around while driving might potentially end up under the furnace.
I think you should keep going. By the time you finish you will know the rig inside and out. You will also know the quality of work done and can be confident in the repairs. We bought ours new and, like anything else, need to maintain and fix it occasionally.
