Hmmmm….it's very difficult to think of a rebuild, as the 98 custom is probably one of the most recognizable paintball guns on the market.
Look at it off hand.....hmm. If you're going to go with a blaster rifle build as opposed to something like a flamethrower (my first instinct on seeing the hose), I would recommend maybe...
1- Stock
2- Longer Barrel
3- Ditch the hose and tank connection at the bottom of the grip
4- Obviously, sand off everything piece of lettering you can find on the gun and chop off the hopper connection point
5- Scope, maybe two side-by-side or one in front of the other like on Bossk's rifle
6- Side-mounted magazine either above the front grip or between the front and rear grips
7- Sand off or remove any Picatinny rail you don't need for the scopes
8- MAYBE remove the rubberized section of the rear pistol grip and replace it with a leather or cloth wrap.
That's my personal opinion so take it with a grain of salt, and obviously there's a nigh infinite number of means to go about doing all of that, but I think that might be what you need to get it to a point where the App team will clear it.