Crank Pulley TDC is an inch off PLEASE HELP

I just rebuilt my b18b1 integra for the second time. I put a skunk 2 intake in and new throttle body. I made sure I was at TDC when I put the timing belt back on. When I started the car up and it was only at 300 rpm’s so it was basically dying after I bit of fuel and so forth got up and going again it was idling fine. Once I rev it up a tad and let off, the idle starts to jump lightly. I was assuming it was distributor timing. Keep in mind there’s no CEL. I look at my crank pulley timing with a timing gun and it’s way off. I take my timing gun and try to adjust it but even putting the distributor as far as it can go the timing mark just wouldn’t line up it’s about an inch off. I thought since my throttle wasn’t right it was making it not line up properly but when I went to increase my throttle on my intake and throttle body the engine wouldn’t stop jumping up and down around 1200-1000 rpm’s so it wasn’t steady enough to line up the TDC mark on crank pulley. If the oil pump isn’t lined up would this cause the crank pulley to be off as well? I was assuming if this was so it would causing valve lash or so and throwing a CEL but I can’t seem to figure it out. PLEASE SOMEONE HELP