Doing the Accelerometer Calib I stuck the FC to a box that was as perfectly shaped as possible, does the size of the box matter? I noticed my "accel bias & accel scale" numbers would differ a little with the 2 boxes I could find that were in good shape.
Size doesn't matter.
I use a similar procedure. Get it as close as you can and don't worry about it.
I also noticed after I would calibrate the gyros and save everything the halt the board and boot up again my gyro scopes would be as flat and smooth as a dead mans heart monitor but after about 60 seconds of not moving the drone the gyro scope would go nuts going from 0.1 to -0.3 , if I nudged the drone or give it a bump the gyros would calm down and back to 0. Is this normal? I have redone the thermal calib hoping that might help but havent checked it yet.
This is just the auto-ranging. That zero is really still jumping around, about .1 or so but there is a large jump on the screen so the scope scale is insensitive. It is either that, or you are commenting that some scopes see zero until initialization is done and it becomes ready to arm.
last but not least setting up the esc's with dshot. I did the whole vehicle and input wizards then to set the dshot i would goto System tab under ActuatorSettings/Bankupdatefreq/DShotMode adjust the Khz to 600/300/150, then under configuration tab/output window/output configuration change the mode to DSHOT in banks 1 thru 3. I noticed in the Output Channel Configuration section the Min was at 0 my neutral was at 1020 and Max is at 1900. then saved, put drone back together put some props on it and held on to it, just barely up throttle and shot outta my hand and battled the ceiling fan. Im guessing my esc's arent calibrated correctly or those #s from min/neutral/max are just a smidgen off.
You must be running 'next'. I haven't used Dshot. I don't know what the legal values are.
I was also noticing some yaw creep when looking at the flight data page and I would notice if I got the drone facing 0 north after a while it would creep 18 to 20 degrees and the drone never moved. This was before i hooked up gps and did a full thermal Calib. so just ignore this part if the gps/thermal corrects this.
Do thermal calibration, and then do a gyro calibration after that. There is a bug and the gyros are off a little after thermal calibration. But FYI, the mags keep it from drifting when you use INS13. But FYI, the mags are noisy, so it will jump around a little.
PS the I2C worked without putting in the pullup resistors (they havent been shipped yet) by putting those on from the 3.3v to both wires does that smooth out the signal to the aux mag? In other words what is the benefit of doing this. So if someone asks me why I did it I have a better answer than "The guy on the forum said to"
Bad I2C can fail in flight which is not good. I would set up a very long term (24 hour?) mag alarm scope, prove that I can see an alarm if it happens (generate a false alarm) and let it run for 24 hours (connected to a 12V power supply instead of a battery). Also, an hour after you start it, look at Firmware -> FlightTime and make sure it is about 3600 (an hour). After X hours it should be 3600*X seconds on FlightTime. If it is significantly less, the FC rebooted (bad I2C can cause reboots).
PPS is it a good idea to have the Zero gyros while arming, check marked under gyro initialization?
It zeros them at power up. The default is to zero them again at arming. This is only used with Basic/CF, not with INS13. INS13 doesn't ever zero them. It uses the stored calibration values.