Hi Zach
Welcome to the world of first time jointer tuner uppers.
I think that you will have to go back to square one for a fix. Before starting to set the knives you have to make sure that the tables are absolutely co-planer to each other
This is done by removing the knives and checking the tables. I like to use a good level because they are, or should be, straight and true. Bring the depth indicator to zero and check the alignment of the tables. Place the level on the tables and check to see if any light is passing under the level. If there is then adjust the infeed table so that the level lies flush along the length of the infeed and outfeed tables. Check the zero indicator and adjust if necessary. Also check the table alignment at three positions across the cutter head opening. They should all be the same. (no light) Then check the tables from corner to corner.
Start by installing one of the blades. The height adjustment screws should be at the bottom of their travel.
Make a calibration gauge by using a straight piece of stock (1 X 4 by 6" long will do) and place it on edge flat across the cutter head opening. Mark vertical lines 1/8" apart on the gauge. When you adjust the blade height you will rotate the cutter head in the normal direction and adjust the height until the blade just moves the gauge one division. Do this on the inboard and the outboard end of the knife. then repeat for the rest of the knives.
When you get close to the desired height you will be turning the height adjustment screw about 1/8 of a turn (or less) at a time.
Always make the final turns of the height screw by backing it out of the hole (CCW) to maintain contact with the blade.
If you turn the height screw CW it may lose contact with the blade and when the wedge lock screws are tightened the wedge lock can push the blade down and you will lose the adjustment.
One other point, The bottom of the cutter head slots and all of the components, (knives, screws and wedge locks ) have to be clean and free from any debris that may get in the way of proper contact.
Check the owner's manual if you have it. I have found that Shopsmith's method is the fastest way and the most accurate of setting the knife height. Also number the blades or you may make my mistake of setting more than three knives on your first attempt.

Let us know how you make out.
Bill V