Sounds like you'll have yours dialed in quite well! My 50mm open marzoocchis were harsh on everything from being super Low in the stroke I think. I had them revalved and they are still a little tough on the abrupt square edge stuff but fantastic on whoops type stuff.
I'm now dealing with the new 45mm KYB. They're a little harsh but not as bad as the marz in stock form. I haven't ridden it since I reset the rear sag. That in itself should make a big improvement and be more balanced. My front springs need to get sorted though, not enough sag race or static but I worry about being too low in the stroke again. After a ride I can see that the tubes go down pretty far on the stanctions.
Just keeping my fingers crossed, but I think I got the Zokes figured out. Dwight has been awesome and a huge help, period! I dropped my springs (6mm preload) and oil wt to 5 like he recommended. The only way I could get my 45's to bottom, was to lower my oil to 140mm (even with the 40 springs). I know, everyone says don't go under 130mm (But how do you get them to bottom). Then I went up 2 clicks like he recommended. Then my compression screws started leaking but I still was harsh on all the sharp, square edged bumps. This bike has always had a problem of deflecting off of stuff at low and high speeds, plus not turning good. My confidence dropped, because I was constantly wondering if the front end was going to kick out from under me. Surprised, that I haven't broke my collar bone yet. I was always on guard looking ahead to avoid stuff and then out of the blue, I would lose my front end.
My forks, when riding, are further down in the stroke, but it feels more balanced and planted. I too was concerned.
I have been keeping an eye on these valves to modernize the harsh issues for 45/50 Zokes. So, I decided to pull my forks completely apart. 3 out of 4 holes in the bottom of the base valves, had burrs in them (From factory machining), closing off the ports 1/4 of the way? Well, one burr was under one of the shims, from breaking loose. I guess my question? Why wasn't this caught, when the forks were revalved. I won't talk bad about anyone, because it could have just been an employee oversight. I did take pictures to back it up and is something to look for?
Last night my new valves got here and I measured the provided shims, and installed them in the new base valves. I also put new seals in my clickers. I was told by the new tuner, to go with a maximum oil level of 125mm/5 wt oil. The valves are huge compared to the Marzocchi ones. They look like Chicago sewer pipes (They have got to flow some oil, now!). He also gave me 5 more clicks of compression adjustment. I rode a couple times last night and adjusted the clickers till I bottomed. I bottomed with the new oil height. Then went up 2 clicks like Dwight suggested. These forks are totally plush, carve better in turns, seem to brake good, but guess what? No, initial harshness on the square edged stuff! Actually, they feel like my old Showas on my old RMZ 250. I still need to do some real, log, creek jumping stuff to fine tune the clickers.
I will do a better post, after some more testing. Also, I still need to go up on the rear spring since I get the sag results but way too much preload, to get there. Now I am getting suspender poor, cause I have to do the Wr 125 yet.
Just a note: I did a good fork alignment thread under General, Tinker Tips. One issue I was having, long ago. The forks would never align properly with the bounce, brake and compress method. I seem to be getting different alignments. So, this is a way I don't have any stiction issues and second guess. This helps out alot in initial, mid and full strokes.