I typically always download the premade firmware for my printer under the Ender 3 SKR Mini E3 V3 BL Touch but I really want to use Input Shaper but none of the premade ones seems to have it enabled. So I then tried to make my own.
I selected the Ender 3 and SKR Mini E3, I left 90% of its default, I simply enabled bilinear auto bed leveling (I tried UBL as well with no change), set the probe to be the probe port, and turned the probe to z homing and turned on input shaping.
I installed it onto my print which seems to work fine however, it keeps on failing/stopping the auto bed leveling roughly halfway no matter what. I tried playing around with settings and it just doesn’t seem to work/nothing I tried fixed it.
If I use a premade one under the Ender 3 SKR Mini E3 V3 BL Touch it works fine, just again it does not have input shaper.
I am not sure what I am doing wrong and why it is not working. Is there a way to modify the premade ones to just change it to have input shaper on?
The fun part at the moment is: Which input shaping? 
There’s two competing methods at the moment - and the tuning methods for each are different and not really complete as yet - although work is ongoing as to which is which and which methods are better.
I wasn’t going to put these in the default builds until there’s some clear guidance as to what is recommended, and we have a proven way to calibrate each method.
Until that happens, it really should be considered highly experimental. Existing methods to tune input shaping might not be optimal, or even correct - and documentation may well be out of date.
As for the probe failures, what message is produced?
I greatly apologize for the unfathomably late response just haven’t had time to dive deeper into this issue.
No error pops up on the screen of the ender, however, when using pronterface I get a super generic error. The error is as follows:
Error:Probing Failed
[ERROR] Error:Probing Failed
With that, it send the hotend/nozzle straight into my bed as well. However, sometimes it just stops, it does not go into the bed or anything it just stops acting like it is done and no error pops up on the screen or pronterface.
Again, the default builds work fine but when trying to build my own using the builder or downloading my own marlin and editing it results in the same. I assume there is some setting somewhere causing issues but I am unsure as to what is causing it.
I’m having what seems like the same problem. I have the same printer and motherboard. I used the firmware builder and had it set up the UBL. It also gets about half way through the probing then just stops. Makes a beep but no error message (or flashes too fast to see).