Hey Robbo! Been thinking about this one.....
First the boot stripe(if any) is not always the water line. Also the ship would sit lower in the water full stock than on a return voyage and 3rd she would be (if I remember correctly) higher in the summer (warmer water) than in the winter months...with all that aside.. You should be able to find some pretty good shot of how she is lying and gauge your cut accordingly. Use reference marks like the boot stripe, port holes, anchor wells to find one single point reference. Try printing out the picture to about the scale you are working and you should be able to match it it pretty close.
From there, prop her up on a stand or makeshift keel clamp so she is sturdy. Then take a dowel ant either drill a hole through it ( if it's wide enough) and slide a pencil through. The pencil should be at the height of you referenced waterline mark. On a flat surface (kitchen table??) you should be able to transfer the waterline (level line) all the way around the ship. A small pen laser or higher end rotary laser works well too. Set the laser to the height and take your pencil and mark your line.
There are formulas ans drawings and blah, blah, blah....basically if you are going to do a waterline series by cutting the bottom get your reference point close to what you see leaving some , cause I could assume you will be creating some sort of water effect. And the rest will come together with listing and waves.
Hope some of this babble helps 
BTW...Which Ship?