I just fixed my crank, put on a new lower timing gear & key. I also picked up a new timing cover because mine was broken & the belt had rubbed it.

I have the belt on without the crank pulley & the belt will walk about 1/4 way off the gears.  It will do this just turning over or with it running a few seconds.  Is it because I don't have the lower pulley on or is something else messed up?

mine was same suzuki mech said just put the pully on itll be OK

It is walking off because the lower pulley is not on.  The pulley keeps the timing belt from walking off the front of the gear.
The reason timing belts rub the cover is because the cover warps with age.  Your new cover will eventually warp too and the belt will rub it....but hopefully that will be many years down the road.

Thanks guys.

I finished it up and got it running.  It sounds like I have an exh. leak now.

Pretty common for the donut between the header & exhaust gets blown out. Mine was a $15 fix... and a lot of frustration getting the bolts off.