Struggling to keep knife flat on the stone

[BPalv]

I have encountered a similar issue about keeping the blade flat on the stone. The blade holder keeps hitting the post of the threaded part of the universal support bar. I am unable to slide the blade holder smoothly along the bar. What should I do to avoid this?

I believe I have been experiencing the same issue (occasionally) as you.  I believe the root cause is the KJ-45 jig.  Is that what you're using?
The collar on that style jig is a tad more than 90° to the USB.  It is flared out a bit causing that.
Someone had a similar issue and just filed off the area it was bumping on the USB support bar.  I will be doing mine in the morning.