4cm is too much, specially for trail braking
If that 4cm is visible tube (mechanical bottom is maybe at 1.5cm tube being visible), then 2.5cm may still be too much.
Don't know gen3, I'm racing gen4 with 2.5cm visible (1cm from mech. botton) and get nice "rear tyre light" feeling at hardest braking.
What is the bike doing or not doing?
Front end "dancing" with hard braking?
Or does it not want to lean over easily and you are fighting it to get turned?
Too stiff springs for your weigth, oil level accidentally tooo high, wheelbase too long, swingarm too flat?
The bike was too hard to ride. I did 8 laps and was exhausted. In March I did 17 laps at the same track and I was fine, a little tired but OK.
I didn't have any feedback from the front, I couldn't tell if it was holding or not.
It was SOOO hard to flick the bike from side to side at the chicane or left to right apexes.
Under braking it was fine but I wasn't pushing it like I can, I didn't had the time to do so due to my shoulder mishap.
Regarding the suspension, I just got them rebuilt by Ohlins in Italy so I know they are OK :)
Instead of asking yourself can I get my bike to handle like the 2015, ask yourself can you get comfortable with what you have. If you can get comfortable on the bike and work with the deficiencies, then generally you will be able to drop time. It sounds like your bike is fighting you more than working with you which in turn is causing issues. Find yourself a good suspension/geometry tuner and work with them to figure out what issues you are having and then work to fix them. If you can sort out the bike you might be surprised how fast you can get.
I actually did find a good suspension guy. I had a race in Misano on last September and I've met a WSBK suspension guy. He was Marco Melandry and Matt Meladin suspension guy :)
He adjusted my suspension but the bike was too stiff.
I met a different suspension guy last week, he was the one to tell me that the bike is way too stiff for my skill.
As I mentioned before, I live in Israel and my bike is in Romania so I can't spend time fixing and adjusting it. I only have 5 days to ride each time I fly so you can understand why I'm short on time.
I love the Gen3 but after only 4 laps with the Gen4 I understood how much better it is. And it is almost stock !
I think I can go down a few more seconds with my bike but I believe it would require less effort to do so on the Gen4.
I spoke to my mechanic and told him I would love to keep the Gen3 and see whats the best I can do with it and then switch to a Gen4 but I'm affraid it is not an option for me. I must decide between the tow.