Thanks for the tips, I calibrated the flow rate as suggested and it was way off. I got it to 107 steps/mm, it was at 138 before. Then I moved to setting the filament size and extrusion multiplier. I was able to follow the procedure and print a shell of box with one perimeter at the right wall thickness giving me 1.75mm diameter and .79 multiplier. I then proceeded to print my first part and I noticed I wasn't getting proper layer adhesion. I only changed these two settings an now all my prints are failing. I double checked the z-offset and it prints fine. But after the 10th or so layer the filament is just loose spaghetti. it's almost like the z-axis is no longer taking the right size steps. Since the z layers are calculated based on extrusion parameters could calibrating the extrusion have ruined the set layer heights?

It sounds like something is not calibrated correctly. Normally that box test would be done at a .3mm layer height at a flowrate multiplier of 1 or 100 depending on your slicer. That should give you a wall that is right around .48mm wide. Your extrusion width by default on a properly calibrated mschine should be around 60% of the layer height with multiplier ser to 100%.

The multiplier is just a bandaid for the real problem.

Another golden but unwritten rule is te never print a layer that is greater than 30% of your nozzle diameter. On a .3mm nozzle you should never go over .27 on your layer height. Mind you its not written in stone but to get proper layer adhesion there is certain necessary amount of squish needed. Of you where to look at s layer crosd section it should br oval with a flat top and bottom. It should not be round.

Since the z layers are calculated based on extrusion parameters could calibrating the extrusion have ruined the set layer heights?

that's not how layer height works.  What layer height are you using?
If .3 try .2963 instead.
You can also calibrate steps per mm for the Z axis.

The first few layers of my builds seem to be off. It looks like a mess, like it's flowing too much filament, bumpy surfaces that make the extruder bounce up and down as it's dragged across it. The first solid layers look great but this mess starts with the first fill layer and goes for at least 4 layers until it smoothes out. Lowering the fill rate doesn't make this problem change at all. It's so bad on some prints that the nozzle gets caught up on a big bump and the stepper skips and kills the whole print. Any ideas?

So lets go with the obvious, is your extruder e steps calibrated properly?