Hopefully someone can help me on this problem. So far I have tried my best to check over everything. This is my second time I had to rebuild the bottom end the most recent was just replacing #6 again, since the rod was burnt cause by some newbie shaved my crank. Last start up was fine but after I replaced #6 and with a new crank. On start up it would start then hesitate for a second or two then back off it went with no idle in less I held the gas down a bit. Which it would have a really ruff sound to it till warm. Plus with a bit of a knock coming from the top end. The part that gets me is that I have good oil pressure from the start. So far I have done a compression test on all cylinders and they are all at 60ish. check the plugs which was bad will be replacing them this week plus a coil was missing it's spring. If someone could give me a idea what it might be or what to do or if it would be best to just take it back down and check over everything piece by piece

60ish is way to low for compression. Especially if you just rebuild the bottom end. You need to do a leak down test. Ur compression should be around 150ish across the board..u need to verify that u don't have a head/head gasket problem not sealing properly, valve sticking ope, start with the basics, ect.