Try these in order (powered jackplate is a given, momentary foot switches are great for operating on the fly):
1) use a SS prop, four-blade with large blade area and double cupping, check with Baumann Props in Houston as they specialize in tunnel props designed for operating in aerated water. If Baumann is not an option, try PowerTech Props. Mike Hood on the TX gulf coast is also good.
2) add an inverted hump, mid-hull, between the pontoons. It can extend as low as the bottom of the pontoons. This will help purge air from water flowing between the pontoon hulls, and make for greener water at the prop. It also has the effect of shooting the water back upward to the prop. Look at good pocket tunnel designs and you will see this feature, a bulbous hump of sorts at the leading edge of the tunnel.
3) add extensions, or pods, to the aft end of the pontoons. Make these even with the hull bottoms on the pontoons, assuming you won't be using this in rough waters. This will effectively extend the length of the hull and prevent the transom from squatting during holeshot, as well as giving lift to the aft end of the boat.
For reference, i run a 26' aluminum flat-bottom with mod-v bow and an 8-foot pocket tunnel in the transom. Engine is 115hp Mercury four-stroke with four-blade SS Baumann Blaster prop with 13" pitch to get motor into 5800-6400 operating range. Holeshot is within a boatlength, noat runs in less than six inches of water over hard sand, three inches of water in soft bottom when on plane. Off-plane, boat needs 10" water to putt around, 12-14" over sand for holeshot, 8-10" over soft bottom for holeshot. With that size of boat (26'), it will carry a lot of weight/cargo and lose very little draft.