Motorcycle Repair: 1986 XL Sportster 1200, retarded timing, oil hose

Question
Hello,
A repair shop rebuilt my engine and now it is a 1200. After close to 500 miles, my bike began spitting and POPPPING and fire was coming out of the short pipe. I cleaned the plugs because they had a pretty good amount of carbon deposit. It still ran the same. I changed the oil and filter. I accidentally drained the primary fluid, so I added about a quart of primary fluid. It was turning over but not starting and ended up flooded. I pulled the plugs and they were fouled with carbon. I put on new plugs (Autolite 4164 gapped at .042). It then started right up. I had read that retarded timing could cause the popping and fire out the exhaust. So I adjusted the timimg. It stopped spitting and banging, and had no more flames from the exhaust,and seemed to idle well. But, it also had a knocking from the left side that seemed to shake the bike too, so I shut her down. The oil pressure light goes off when it idles. I checked the oil level and it is too full. I am going to loosen the bottom oil hose and drain the excess oil. Do you know what could be causing the knocking? I am also unsure if I have enough primary fluid  because the oil level plug has been replaced with a makeshift plug which was JB Welded. When I put my finger inside the filler hole, I can not feel the oil, although it is oily in there I can't feel the "top" of the oil level. How can I know if the level is good without a removable oil level plug?
Thank you,
Suzy

Answer
First, you plugs need to be gapped at .040, not .042.

Your plug for the primary needs to be repaired, so when it time the change the primary fluid you have a way to drain it. There is no dipstick for the primary, when you change it you put in 32 ozs.
I am going to assumn that the bike ran fine up to 500 miles and then the plugs started fouling and the knocking started.
If your plugs are fouling it could be a bad coil, or worse, a bad piston. You can test the coil and do a compression test on the cylinders to determine what it it.
As to the knocking, it could be a bad rod, bad piston, or preignition. Again, you would need to do a compression test and a bleed down test.
Good luck and happy riding
Mike