If I removed the crank pulley off with out the holding tool, would it mess with timing if the pulley moved before the bolt got lose . After I put everything back together I started to have long crank ? Or can I just be having another issue. Like fuel issue ? I also installed new battery and crank sensor.

 

If the only thing you did was to remove the crank pulley, it wouldn't affect your timing. The pulley itself doesn't really have anything to do with the timing other than to hold the crank gear in.
You should be fine as far as that goes

 

So I was told Honda’s have long crank in general, just gotta turn the key and give it couple seconds before starting and it should be fine. It’s starting fine now but I feel like there still might be an issue . Cuz I think the starter is shorting since I smell burn at times.

 

starter only drew 30 amps, replaced starter and fixed issue!