So sometimes you need to convince things to it flat. That is what the strap and clamp are for. Minor adjustments before tacking the bits together. To get it all lined up and level I am using 3" screws to put it together. Don't worry I have plenty of dowel rods and glue coming once it is level.
Time for the top. After attaching the top with screws I drilled the first pegholes. Then I used a brad to mark the other holes. Beat the top down on the pegs and the brad marks the top for the dowel. Beat it loose, flip it over, drill the dowel holes and we are in business.
Here you can see the dowels that go through. I use the 3 inch screws to keep it all snug but I don't really need them. I had to beat the tops onto the pegs with a deadblow and a 2x4 scrap.
Don't mind the long runner sticking out it is jet to keep it square while I get it pinned together more permanently.
On this side is were the leg vise is going. Still a lot of work to do but at least it is usable now.