I honestly think this may be a result of steps per mm being of in firm ware.i believe in a x or y only axis this Mar be harder to see a one motor may compensate for the other. But be measuring angled distance this could be revealed. Then again I may be wrong.
@D_Rob I ran a 40 mm L shaped steps per mm calibration piece last night oriented at 45 deg so it only requires 1 stepper per direction. Accuracy was 40.08mm on stepper 1 and 40.18mm on stepper 2. I need to get those values into marlin tonight… But I am not sure if those results are good or bad. They seem pretty close.
Take one of your cubes not printed on a 45 and measure it across opposite angle corners. Square the value. Side 1 squared x side 2 squared should equal that cross measure squared. Like I said this is a theory and may not reveal your problem. But if there is a problem in steps per mm not revealed in traditional ways this definitely will. I will say stepper two needs recal but 1 looks good. .08 is ridiculously minute and shouldn’t be the issue but with the angle changes in a circle and the fact they use both motors stepper could cause this.
I am losing hope. Extruder jams all the time. Prints are slanted now. Bed won’t reach abs temps. Bed crowns when heated (at first I thought it was just my cheap glass).
I cannot even get prints running as well as I had the first day I tested my printer.
All and all a crapsastic night 
@Eclsnowman The crowning is an issue I’ve heard of with the silicone and polymide heaters. If you tape directly to the glass the glass warps. If to the plate it warps. Best way I’ve seen is lay the heater without adhesive on a surface MDF or wood (an insulator) then lay an alu plate heat spreader on it these can be sandwiched with nuts and bolts. Then glass on the plate. I am using a 22ga 12x12 sheet metal panel then insulation then ⅛alu sandwiched with bolt and nuts at 3 point the excess bolt is for leveling.
@Eclsnowman is the extruder jamming? The hot end? Or is there striping and you assume its jamming?
Can you list some video and/or pics of it “jamming”?
It jams after the first several layers. I think I need to look into a cooling fan on my direct drive extruder. I think the motor is heating up and softening the filament.
@Eclsnowman Some nights are just like that, don’t loose hope. Also remember you are not on a clock, it takes as long as it takes. This is all hard earned advice btw - I have had some shocking evenings over the last few years.
Don’t loss hope - it might just not be as easy as you expected but the hard lessons are the best ones and the things you learn solving these problems all contribute to a better understanding of this thing that came out of your brain.
If at all possible - go back to your starting point and change 1 variable at a time. Be scientific, don’t allow frustration to get the better of you and all that sagely BS 
Also, try a different slicer if you haven’t already.
I forgot to explain the why of the crowning. the adhesive keeps a constant surface to surface contact. thermal expansion is to blame. It’d like the bimetallic switches in thermostats one side expands faster than the other causing the coil to wind and unwind. Or if straight to lean one side or another. The heat pad expands at a different rate than the surface is adhered to causing the surface to bow like fried bologna
@Eclsnowman , we’ve all been through the same hard times buddy. Your 3d printer is like another wife, at a certain point of conflict you need to know when to walk away before causing more damage. We’ve all smoked parts and broken components due to rushing, tired hands. Like @Tim_Rastall said, troubleshooting needs to be slow and methodical, one variable at a time. This is also how you learn how your printer behaves. I’m sure you have a far better understanding of how it works now then you did a week ago.
As for your extruder, I always test it extruding in free air to remove a bunch of variables. I just keep dumping filament through using my host software. If it is in fact your extruder gear softening the filament, the amount of filament being pulled from the spool will increase. You can mark lengths on the filament with a sharpie and measure how far it moves. See if it changes with motor heat. I have the pgl35 motor with a fan on it in a Bowden setup. My motor was getting ridiculously hot, and 10 minutes or so into a print, the print would be over extruding, then the extruder would jam up when the filament buckled up. Make sure your current isn’t too high on your extruder, as stepper motors are constant current regardless of motion or load. And a fan is never a bad idea, just make sure you don’t cool the actual hot end of the hotend.
Good luck, keep up the good work. Now you can probably see why I’ve been procrastinating my build till others have gotten some builds documented. I can’t thank you enough for taking this on and posting about it.
Thanks everyone. I needed to vent. It has been rough feeling like you are moving backwards.
There’s another reason not to rush – the entire system may take more than a couple of minutes to reach thermal equilibrium. Sometimes, you just have to let the printer warm up and idle at (or close to) working temperature for ten minutes and then tram / gap / calibrate as needed. If your HB sandwich is bolted together, make sure its bolted at operating temp, not room temp. The differential expansion will (as @D_Rob pointed out) will cause curling.
@Joseph_Chiu thanks. I will try that tonight.
I have my 24x24 lexan panels from Amazon now. Hopefully that will help minimize stresses when equilibrium is reached. One question… How are people who have enclosed their printers dealing with the enclosure heat affecting the electronics?
Also what does the group thing about my idea. All panels will be attached with magnets instead of bolts. Easy removal
If you look at my photos you’ll see the base box is closed off and there are fans inside. And for the few holes from one cabinet to the next use silicone where you can and positive pressure from the fans will do the rest. I also plan on using 12v heater or hair dryer from the base to increase fresh air flow for my electronics cabinet as well as heat the build area
I also used 6mm plexi and ran it in the tslots and used a little silicone to prevent the rattling
I’ve yet to put sides on mine as I’m taking things apart and changing stuff too regularly. My intent is to do what @D_Rob has done and separate the electronics and water cooling in the base. of the bot with fans and air filters on the sides. The extruder steppers are on the outside of the bot so they don’t need to be cooled and I’m going to use a cooling chimneys like on the Ultimaker 2 for each of the drive steppers.
@Tim_Rastall why not just mount the drive steppers on the outside? With pulleys instead of gears it doesn’t take much more room. Mine are currently in the front right but they will be relocated to the rear when I print the pulleys you fixed for me. Ty by the way.
What are you guys planning on doing for a top? That’s the one that still has me thrown for a loop.