I'll take a crack at this, but remember that I am an Idiot and my advice is worth every penny you pay for it. Additionally, I have not stayed at a Holiday Inn Express for quite some time. And I am not an engineer!
There are quite a few folks that add additional 'flotation pods' to the transom of their jon boats to either 1) help support the additional weight of newer four-stroke outboards, or 2) make up for the buoyancy lost when running a pocket tunnel hull. In these cases, the motor stays in the same position on the existing transom and they are simply adding flotation and additional planing surface to the boat. I know it's like comparing apples to oranges, but some of the concepts remain the same.
In almost every case, boaters who have done this really tout the benefits. The back of the boat rides several inches higher and the hull planes quicker. The tricky part for some is that if the bottom of the extensions are even with the bottom of the hull, then you can't raise the bow of the boat to take on larger waves (remember, the outboard is still in the same location, with some planing surface BEHIND the motor - a side benefit of this is that it generally cures any porpoising problems). To combat this, some folks will angle the extensions up a few degrees to get their trim range back, but then they lose some of the benefits of the extra planing surface. On a larger boat, it seems to be a moot issue and the extensions can be kept even with the bottom of the boat.
In your case, you are moving the engine back also. Therefore, you shouldn't have any issues with trimming capabilities, and should reap the benefits of a greater planing area (e.g. - longer hull). Just be certain that your 'new' transom can handle the pressures that the engine will put on it. It is definitely better to over-engineer in this area. Existing transoms have the benefit of having the sides of the hull tied in to greatly strengthen them.
I believe the boat will also be more of a 'pig' when it comes to slow-speed handling and maneuvering. You will have more leverage for turning, but the longer hull will take some getting used to. Depending on weight distribution, you could also end up with porpoising problems, which you may have to eventually fix with trim tabs since you will be dealing with a modified hull.