Something hasent been assembled correctly by the sounds of it. Gnasher may have some input, but you should NOT have had to modify or create a work around to reassemble the forks. Did you follow the manual? - https://www.manualslib.com/manual/659471/Yamaha-Fz1.html
The way I put forks tops back on when the spring pre-load makes it hard, is to place a bit of cardboard/carpet under the bottom of the fork to protect the end and then use my body weight to push down with one hand then and then with the other hand make a wide arc (1/2 of a single turn) on the spanner to get the thread started.
It's all assembled correctly, probly done hundreds of forks over the yrs, defo spring/inner stanchion contact, all springs rub, hence grey fork oil when u drop it, stick a magnet in old fork oil, it'll be covered in metal bits.
Just a bit noisier than expected, 1st time of using K-tech stuff, might be my last, I'm not the only one with experience off tight K-tech fork bushes, no way would they go in without opening up the end gap by 0.25mm minimum, still tight but went in without too much of a wollap from my bush fitting tool.
It's only audible bouncing forks, can't hear it while riding with a lid on.
I'll suck it n see for now.