Just started up my 89 Baja with a 3 year old 454, I have a knocking noise coming from the back of the engine and a ticking noise from the port valve cover. The engine oil level is high and I will try to lower it to just over full. I will check the flappers as I see they are a source. I am running the engine on ears in my driveway and will also try lowering and straightening the lower unit. I am not very engine savvy and any other checks you could suggest would be great before I take it to the mechanic. The engine starts well and idles smooth with this noticeable knocking that gets greater as I reve slightly. I just changed the plugs and will check to make sure I did not switch the wires as well. I have a hydraulic cam and no roller rockers. When turned off I checked the shaft out the back and there is a tiny bit of movement when I press on it with my finger, is this normal? I could take off the valve covers and check things but beyond this I am out of my league.
Any suggestions?

Flapper noise typically goes away when you rev it up.

Is it more of a tapping sound or knocking? High on the engine or low?

Ok, if I read this correctly, you have the drive trimmed all the way up? If so, dont do that. You may have hurt the u-joints already. Trim it all the way down and start over. Dont get too excited about the ticking noise yet, it may just be a lifter that hasent pumped up yet. If it stays, pull the valve cover and adjust the valves. That may do it.