Shale we do some deductive reasoning?
The first look at these 'suspect' loaded cases. What does the new to reloading loader see? "not all of the primers are not fully seated in the brass" & "definitely are not flat across the cartridge base and will rock when set on a flat surface" (your words). As stated above, 'that ain't good', my words.
Let see.... do we/you want to chance that these loads are not going to blow up our costly weapon... hand... head? Quality workmanship on those primers give me less than a warm feeling about the rest of that load.
Now that that has been determined. Pull the bullets, there are many ways to do it. The powder purchased with this was Hogdon Clays. But is that what was put into these cases? Revert to the above logic. Small amounts of smokeless powder burns pretty (in a safe and open location - concrete is good). What about those primers? Only 20 or so.... I would play with them. Safe and empty weapon, pull back the slide and lock it, drop one (1) primed case into the chamber. With the barrel pointed in a safe direction, drop the slide, just push the slid lock down and let er fly. Did the primer pop? If not, pull the trigger. You now have brass with a dead primer, ready to start the loading process.
I don't use any of the 'Clays'. With that said, start at the 'starting load' listed and work from there. As long as the scales are consistent, don't over think the process. I would 'zero' the scales and load the 'starting' amount of the selected powder in accordance to what is listed in your trusted reference material. Don't load more than a sampling. Test these. Two round in a magazine, load from that magazine, fire the first. Did everything happen that is supposed to? Eject, strip the next round, chamber the next round? Fire the next. Did the slide lock back?
If all did not do as it should, determine the problem and correct (too light of load to function? seating depth or feed ramp not mating?)
Slowly adjust your charge/s until you get the loading that meets you desired results. Remember, the listed MAXIMUM load is not a challenge.
Load with care and enjoy,