Some tunnel hull boats are not designed for use with a jet,such as the Alumacraft.The tunnel is too deep and does not perform well with a jet.Lowe(Roughneck) tunnels are designed for jets.They have a web site and have a nice rig specifically set up for jets.There is a debate about weather you really need the tunnel if you are going to use a jet.With a tunnel hull you lose a little bit of lift that would make up for the inches that the intake sits below the bottom of the boat.(6 of one,half a dozen of the other).Another consideration is with a tunnel the intake will not hit as much because it is above the bottom of the boat.Well if you end up going over a rock that would hit the intake on a flat hull,its still going to hit on the tunnel hull.The boat will just ride over it and it will smack the intake.The tunnel hull may actually direct debris to your intake by the angled sides of the tunnel itself.My rig is a flat bottom and I have hit plenty of obsticles from logs to boulders.Logs are nothing,you just skip right on over them.I don’t even look out for those any more.Rocks do give you a bit of a jolt and have dinged up the intake grate but the intake grate is made up of replaceable fins and are cheap.
If you go with a flat bottom design make sur that the boat you buy does not have a center rib or strake on the bottom of the boat.This will create bubbles and your jet will not perform well.The area that the intake sits behind should be flat with no obsructions.I have a G3 that is designed this way.
One manufacturer I would suggest checking out if you are interested in a tunnel hull is Koffler.These are not jon boats but a flat bottomed vee with a tunnel designed for jet use.If you are serious about jet rigs check out Fish Rite,Duckworth,Formula Vee.and RiverPro.These are serious jet rigs for the river and all have web sites.
Mercury,Yamaha,Johnson and Suzuki all make jets.You may not find them in their catalogs or at their websites but do make them.You can also get kits to convert your own motor to a jet from a company called California Performance.Merc and yamaha seem to be the most popular.
The debate on prop vs jet is a long one.After going through many props each season fishing the Upper Miss and Minesota rivers the jet just seemed to be the answer for me.I did consider the Alumacraft tunnel with a prop motor but went with the jet.If you want to talk to guys who really know shallow water rigs check out some of the smallmouth bass websites.I would give you the link but am not sure of link policies on this site.