Okay, seems like its running correctly now, at least on the trailer it does. We will see once its in the water. I still have to purchase the inductive RPM reader to verify the idle speed is set right. Once I got the pop off correct according to the manual it ran well but when you hit the throttle it bogged down and died mostly. Mikidymac mentioned the accelerator pump so I checked that and sure enough, the nipple that goes from the pump to the carb throat was busted and not giving a good seal so not only was it leaking fuel in the hull but it was not getting in the carb. I ordered a new fuel Moroso fuel nipple for $3.50 and installed it tonight.
So, to recap my issues from the start.
1, the carb was dirty.
2, pop off was wrong.
3, used a knock off Amazon carb kit, that was the wrong choice. USE AUTHENTIC Mikuni carb kit. There is a difference!
4, verify the check valves are installed in the right direction. They have a curve, the curve needs to curve down toward the carb plate they install into.
5, cleaned the pilot circuit again since I did not do a good job the first time. Note: do not rely on sonic cleaners like I did, spray carb cleaner and verify cleaner is flowing strongly. I recommend Gumout with Regain carb cleaner.
6, once the Mikuni carb kit was installed, the check valves were in correctly, and pop off was correct, it ran and idled correctly. Even easing on the throttle was fine. However, hit the throttle quickly, it would bog down and die sometimes.
7, Accelerator pump outlet nipple was damaged. Ordered a new one from Moroso and installed it.
Now everything seems fine. Time to put it in the water and try it. I hasn't seen water since 2015!
Thanks again to everyone who has helped my and offered their advice. Now, time to rebuild the next one a 1999 GSX Limited.