Swapping a Honda 50 for a 90?

[pontoonboater]

We got a 20 foot pontoon with a Honda 50 4 stroke. It is just not fast enough. We swapped around propellers a bit and lowered the engine--how ever I am not sure if we have long or short shaft (can this make it go a ton faster?). We want to put a different engine on it and sell ours. We are rated for a 90. How hard is this and does any one know if the controls will swap over or if we will have to buy new controls? Do we have to put a honda on it or can we get any kind. What new controls would need to be purchased? I am just trying to figure this out in general b/c it may be worth it just to sell the whole boat and buy a different one.