We are doing a shower pan on the second floor and of course there is plywood already down.  Problem is that there are many pieces coming together under the shower so there are seams in the floor.

It is extremely un-level and I wanted to use a self leveling compound.

First question, can this be used on wood floors?  Second question, how do you seal the gaps so the leveling compound doesn't leak out?

Andy,

How thick is the current plywood floor? How many pieces? Do they go out beyond the shower? Are they glued to the joists? Can you screw them to the joists? Without seeing the situation, I would consider an additional layer of 3/4" ply glued and screwed to the existing floor AND the floor joists, then do your leveling being sure to completely support the the pan. 
And, yes, you can put a solid surface pan on a wood floor system if it is a good pan and a good floor.

The existing is 3/4"

I can screw them to the joist without a problem.

They do go beyond the shower so I can't remove and replace.

I think I will add the additional 3/4" piece of plywood. Do you know if self leveling compound is designed to stick to wood?

Not sure Andy, check the lable or place where you get it. It probably depends on the brand and composition.

I would make sure the existing is in good condition (no dry rot or water damage) then level a pc of 1" plywood on top of that and make sure to hit as many joists as possible, then just silicone the pan down to the 1".  I would want the pan to be able to move if it wants to and also for it have a built in curb on all sides.  make some cool trim pieces to cover whatever of the 1" plywood is still visible after whatever flooring system they use is installed.  Make sure the trim is siliconed to the pan/curb only.  Think wood flooring with base shoe.

In Australia we are required to water proof the floor so we use a system provided by Ardex or equivalent. You use a woven polyester cloth to cover all joins and cracks then cover with the liquid that water proofs the area. After using this you can use your leveling compound no worries.
P.S. you must be licensed to use these products in Australia.