Thanks for the comments.
My plaster mold came out pretty good. Glassed it the other day and my new seat pan popped right out, there on the right. Re-fitted to seat pan and drilled my bolt holes. Fitted or rather it fell in the box half like a glove.
Smoothed the edges out and bolted the bottom half to the seat pan again. Then added the top half after cutting a hole for what will be covered with a lid.
I then made sure it fit level and well on the bike. Removed it and started glassing the inside seam between the two halves.
I removed the seat pan after the inside seams dried and glassed the outside edges and gaps.
I'll let it dry over night and smooth the edges out again. I'll also make sure the fit on the bike is good and then I'll be ready to use bondo the smooth out the whole box. Looks like the back next to the rack will need to thinned out some, just a bit too close especially after adding bondo.
I need to think about how I'm going to do a lid and I'm considering it being water tight, we'll see.