1jz gte bottom end problem!

[Phil haas]

I recently decided to do my vss, I figured I would do some other things while pulling the head off. Once I pulled the head I did the vss, along with gaskets, bc springs and retainers, arp head studs etc. looking at the pistons they didn't look that great but figured I would hold off untill later to build the bottom end, after hooking everything up I started it right up than I killed it after about 5 seconds. Went to start it again and crank crank thud. After that I pulled the plugs and found a good amount of fuel sitting in 5 and 6. Tried manually cranking the motor and it had a rough spot right when the crank pulley would hit 0, I figured it was a stuck valve so I pulled the timing belt and the head spun fine while the bottom end had a rough spot at 0 at the crank pulley. Any idea on what it could be before I pull the motor and find another bottom end?? Note. Camgears were lines up and the crank pulley was set at 10 when we put the timing belt on and later was told it was supposed to be set at 0?