Six inches is probably about the minimum you can run with your current setup while on plane. You'll probably need twelve inches of water to get up on plane.
There are several things you can do to improve performance. As mentioned earlier, start with your cavitation plate even with, or slightly above, the top of the tunnel. Electric-hydraulic jackplates are almost a must-have to get the most out of your tunnel and motor.
A jet won't work with your prop tunnel. A jet tunnel should be no more than three inches deep, otherwise you'll get too much cavitation. You could maybe fill in your tunnel with bondo or something to get it to three inches in depth, then try the jet motor. Avoid jets if you run in vegetation or very sandy (sugar sand or powder sand) rivers - they work best in rocky rivers.
Run a cupped prop. Many owners report best results with a double-cupped four-blade stainless steel prop. The cupping helps the prop get a better bite on the aerated water coming through the tunnel and provides more thrust. Merc makes the best factory props; since you have a 'rude, you might find a Michigan Match or Quicksilver that will let you mount a Merc-style prop on your engine. If you got a little more money, get a custom prop from a good custom shop, like Baumann - they can set you up right, and you will have a much better prop than OEM can provide.
If you are looking for more performance, a lot of folks drill a hole at the leading edge of the tunnel and run a hose from that hole to the back of the boat and over the transom. The idea is to let air into the tunnel, which might seem counter-intuitive, but it breaks the vacuum in the tunnel and lets the boat jump up on plane quicker and run faster at WOT. However, if you do this, you will really need a cupped prop, maybe even a semi-cleaver surface-piercing prop. Do a search here http://refugeforums.com/refuge/forumdisplay.php?f=10
for more info.
Many folks (and more and more manufacturers) put floatation pods on the stern to offset the loss of buoyancy created by the tunnel. The pods also increase the effective running plane of the boat, thus improving efficiency. You might gain an inch or two advantage while running in shallow water.
Trim tabs are also nice to have, but can be a maintenance issue if you run rivers with lots of obstructions. They work on little boats just as well as, or even better than, on larger boats.
My experience with mud motors is that they don't provide the same performance as an equivalent HP outboard. For example, a 25hp outboard will give you better performance than a 25hp mud motor, especially if pushing a load. The mud motor props seem to wear quickly also, and decrease performance further. They are good for getting around in muddy swamps, that's about it.