Depends, but not too difficult.
A. What kind of toilet is in it? 1.Porta Potti? 2. Airhead? 3. Plumbed toilet with maceator, holding tank, and plumbed outlet on gunnel? These are also in order of difficulty to remove, from super easy to somewhat difficult and nasty to boot!
B. To build the seat box, seat back, and table,, etc. is pretty straightforward, if you have the tools, skills, and so forth. You also need to be able to tab (glass) the plywood panels to the hull at the sides and the bottom. Rather than re-invent everything yourself, it would be easier to have a nearby boat of the same model to make templates from, although you may want to make modifications.
C. Next question: Would it be easier to just wait for a boat w/o the head to come along, or is the price or something else a real motivating factor? Just asking....
D. Be sure to pencil out the remodel costs carefully, boat projects are known to often cost 2x-3x or more than anticipated, especially to new boat owners. Then too, there are always added costs that are not anticipated, for new and old salts alike.
E. Also, if you do a professional like job, no problem, but if the craftsmanship is somewhat less than that, it may well, in fact, will affect the resale value of the boat.
Good Luck!
Joe. :teeth :thup