wow - its hard to say from just looking at your pictures, not sure where to start (with my comments).
First off - there is no indication from your pictures that you do NOT have a trap for the shower. They are usually below the slab.
Next - You have moisture issues beyond the leak you had. Make sure all grading outside slopes away from the house, that downspouts extend 6' out and that gutters are not clogged and overflowing. That may address most of the moisture issues (cant say for sure)
I would then draw up a plan. It doesn't need to be elaborate. Just draw out the final space constraints and figure where stuff needs to go. There are books on bathroom planning that can help. The books sometimes even have little cutouts of the cabinets, toilets, sinks, etc to help you place them in the space.
Once you have a plan you will need to continue demolition. I would take everything out, down to the block and concrete floor. Re-do the plumbing rough-ins to the new locations as dictated by your plan, etc. Essentially start from scratch.
You may find some useful tips here Basement Finishing Series
In particular listen to episode 16 and 17, all of them if you have time.