I have used JB Weld Plasticweld Expoxy putty, It's a 2 part putty that you kneed together to activate and it dries rock hard. It's great for building up and filling in the gaps and seams, but it's not easily sandable so keep that in mind and use sparingly.
Sometimes those 2 part vac shells don't line up exactly flush so if you clamp the two halves together, you will likely have issues with the top and bottom edges of the shell lifting upwards and it won't sit flat on the motherboard once the epoxy has dried... I would try to epoxy them together with the shell halves laid flat on a surface face up. You will also want to rough up the two edges that will be joining together with some heavy sandpaper for best adhesion.
Here are some great threads that show how some of us have joined vacu-form shells together:
viewtopic.php?f=2&t=37426viewtopic.php?f=2&t=40187viewtopic.php?f=2&t=38641 Also FYI, the GBfans shop motherboards will almost certainly not fit the 2 part vac-form shells. They are sized slightly differently and won't line up. Most people who do the vac-form builds end up cutting their own motherboard from MDF or some sort of plywood.