TL;DR: Necro bumping this thread as I've found something that could help some people.
You can adjust 3D calibration manually, even outside of the range that the console settings app offers.
Disclaimer: Be aware that this is unsafe and could lead to issues, blame yourself, not me

And backup backup before attempting anything.
Basically I had the same issue as OP, terrible unstable 3D.
As I've noticed that going to console settings and manual calibrating 3D to max 1.0 value was improving the situation, I thought it would be mis-calibrated, especially as the console main board had been swapped by its former owner. I was convinced that if I could push that calibration setting further my problem would be solved.
Found some HWCAL files that supposed to match my console but applying them didn't make any positive change.
So I've did that stupid little experiment:
1. Reset the super stable 3D calibration in console settings.
2. Backup settings partitionA.bin using Godmode9 as explained by TurdPooCharger in this thread
3. Set the super stable 3D calibration in console settings to its max 1.0 value
4. repeat 2. Backup settings partitionA.bin
Diffing these two binary files revealed one particularly interesting byte at
A9F2 increasing from
95 to
B5 (+32 in decimal)
Assuming this was that 1.0 settings value that I wanted to push further, I've edited this partitionA.bin value to
D5
(Simple hex maths: 0x95 (0.0 setting) + 0x20 (+32) = 0xB5 (1.0 setting) + 0x20 (+32) = 0xD5 (should be 2.0 setting))
And... it worked, poof issue gone, super stable 3D working.

I guess I've been very lucky there
Be careful if you try something similar to at least backup you config save partitionA.bin first.
Going again in the 3D manual calibration shows 0, but as soon as I change the value with the slider the issue is back. So you shouldn't touch this setting once set manually this way.