To create extra space in the frame container to hold 18ah (54v x 6  3ah packs)  the container will sit over the top tube frame of the bike as well as inside the frame triangle.  I will now have to make semi circle cuts at each end of the moulds so it snuggly fits over the top tube frame.
To do this will be a bit of a pain to get correct as the top tube of the frame is an oval shape.
I will try and get the exact shape by moulding some foamex strips around the top tube to get he exact shape needed before I cut into the ends of the mould, this will be the tricky bit to get right. 
I am going to use some neoprene beading around the edge of one of the mould sides and some around the holes I have to make to go around the top tube of the frame. I will then need some kind of fastener, nut and bolt if necessary to bind the two halves together to make it water tight. I would rather use some kind of fastener/clip to secure the two sides together for easier access to the lipo packs for balancing but as you can probably tell I am making it all up as I progress 
 
 I have not found a suitable clip yet.  I need something like a jar clip fastener  like used to seal large kitchen jars.    If you have any ideas of what I can use please let me know.  I really need to get to a fastners producer, I believe there is a place in Cardiff I can go to with my problem.  
This is a long term project so don't expect any finished results soon.   I really am making it up as I progress.  It has not really cost me anything but time so far as I used spare pieces of mdf  and got the foamex from school as an experimental project. 
I wish I could add some diagrams but don't have the means to do that on my ipad.
I am a bodger rather than an engineer but I love  problem solving in situations like this.