Python, the machine shop will need the pistons first in order to bore and hone the jugs. Pistons can vary slightly in size and therefore the machine shop will actually measure the piston and machine the bore to the proper specs (that you supply) to accommodate the supplied piston. The pistons are stamped with a number on top of them to let you know what bore size they are so you order the correct pistons for the next oversize.
In the photos you supplied...the picture of the exhaust appears to have had water sitting in it for quite some time and you ask "is this normal" in the caption. The answer is yes and no....yes it's normal if you've flooded it and never blew the water out of the exhaust afterwards...and No it's not normal if you take care of your stuff. Given this...keep that boat taken care of after you get it cleaned and repaired.
On the pistons....the rear appears to have leaned out, gotten hot and melted the edge of the piston. This can be a common problem on Doos on the rear cylinder. You will need to rebuild the carbs to make sure you don't have another failure. Also, you might want to consider replacing the fuel pump on the front carb, that supplies fuel to the rear carb after the front carb gets its fuel, with a dual output Mikuni fuel pump that will supply equal pressure to both carbs at the same time regardless of carb condition. When the diaphragms inside the fuel pump begin to age, they start to lose their efficiency and gradually begin to flow less fuel. In the grand scheme of things this is ok but when the diaphragms are near the end of their life they will only flow enough fuel for one carb/cylinder. The fuel pumps are very easy to install and a bracket is made to mount the pump on the front of the motor next to the carbs.
So, in my opinion, this is what you will need to do a quality rebuild:
2 pistons. Go with Pro-X
Top end bearings
2 carburetor rebuild kits
1 Mikuni fuel pump, mounting bracket and some fuel line
Associated gaskets
Machine shop services
Some grease (for o-rings) and sealants (for gaskets)