Have you tried removing the filter from the shop vac, it could be clogged up......or if it has a float ball to keep water from getting into the motor might try removing it also.
The small hose should create MORE suction.
Are you running the cut out shim? If so are you putting duct tape on the opening where the screen slides in, give that a try also.
Do you have weather stripping on the edges of the vac boxes?
With that big of a vac leaks should not be a problem...........try this.......light your smoker and puff smoke around all of the joints, watch for the smoke to be pulled into the vac box, there will be your leak.
What size hose do you have from the shop vac to the sliding lid?
I found that rubbing bees wax on the edges of the of the sliding lid makes it work easier and also seal just a tad better. With that big of a vac it should pull the sliding lid down tight though.
Just a few random thoughts on it, I have built several and all of them worked great with the exception of one, seems the lid was a bit loose fitting.
Try the smoke, it will show where your leak is at.