I didn't mess with the shift linkage.
When you say misalignment of the actuating arms, are you talking about these points?
What could cause them to be out of alignment, or otherwise change from factory positions?
Someone before you might have.
Someone removing the linkage, perhaps to change the chain, and not putting it back on with the input shaft arm in the right position, not knowing what is wrong, then playing with the actuating rod length to get the shift tang back where it was before.
Someone excessively changing the height of the shifter tang, perhaps for a high toe box boot or a really low profile running shoe, and just using the actuating rod length to get the change.
My son's first ever engine job was a GSXR600.
Stripped down to the last nut and bolt.
After the engine was in the frame, with chain and rear wheel on, I told him to check the gearbox for shifting by making sure it would index nicely in all 6 gears plus find neutral easily.
Uh oh......... it didn't work.
He was ready to weep, thinking it all had to come apart again.
I suggested he look at his linkage...................
The upper arm was out of position on the input shaft.
That took care of it.
In other words, it's a real problem that can cause trouble, and few know about it.