Lately I've been doing multi part prints or parts that are simply meant to be friction fit. However even when scaled to proper size if part needs scaled the holes or contact surfaces never seem to match up. Is there a setting in cura I'm missing or something I can calibrate on my ender 3 to improve the tolerances.

Even if your extruder is accurately calibrated, you may need to adjust the flow rate to tweak the actual line width laid down for different filaments. A puzzle piece is a good test object. If fit is too tight, reduce the flow rate. If the fit is too loose, increase the flow rate. You may need to be at 90% for one filament and 105% for another.

Check thingiverse for calibration objects, you only need to print maybe 10 layers or so for fitment testing.

You should also print calibration cubes to test dimensional accuracy. If the cube dimensions are off on one or more axes, you might need to modify the steps per unit on one or more axes.

Already calibrated the extruder but good tip on the flow rate. I will have to fiddle around with that

Look under the experimental tab and read up on the slicing tolerance settings maybe?

I ran some calibrations and experiments with flow and flow rate compensation and found that flow rate compensation didn't seem to have much of an impact but if I dropped flow to 90% across the board in Cura I got closer to the desired result in the calibration object.  Also recalibrated my extruder and got pretty damn close to the setting i needed there. The second test object which was fitting an S shaped peg into an S shaped hole. I found that Horizontal expansion to be the setting to help with the actual fitment.  So now maybe I can get back onto my original project and get a working result. And I feel like Garrus in mass effect for all the calibrations I've ran and how much I used that word in this post

It doesn't mess with the steps it just provides an offset to help you adjust the size of holes that aren't sizing properly when the outer dimensions of the part are fine. Chep probably explains it better than I can

IIRC, there's also a cura setting for how it slices the edges of a body. Inside the edge, outside, or middle of the edge. That can affect some tolerances as well. I think it's one of the experimental settings. I've always kind of had to fiddle for really fine tolerances. Sometimes it's easier just to put in some horizontal offset, but sometimes you really need to edit the original file. Holes are almost always going to be out of round and out of spec. Especially vertical ones.

I know that my prints just come out about .2mm undersized on the inside dimensions of holes.

10mm hole in drawing will come out as like 9.8mm from the squish I get.

Exterior dimensions are super close to a spec on design drawing.   Like a 20mm test cube will come out to like 19.98 or 19.95.

I am not messing with anything setting wise, like esteps, that will mess that up.

So I just account for it in my designs.

4x4mm square that I need to slot inyo something?   Then I make the slot it is going into either 4.2x4.2 or 4x4.2 depending on if two edges are comprised of top/bottom laters or if all 4 edges are walls.