Tony is correct. We have done all this on a customer's bike, but it gets expensive fast Shorter rear, but then high-speed bumps don't enjoy the full travel of the right-sized shock.
What front do you have? On a cafe, you can move quite a bit but again like Tony said you get close to the cooler. Otherwise, you can lower the front with springs and move the tubes until they almost touch the bar and then deal with the cooler spacing
On the cooler, a step-up adapter pushes the cooler out and up about an inch if your steering lock is close ratio like many 961 are and then you just need to run new hose from the bottom of the oil pump to the cooler. When we did this we also looked at the possibility of turning the cooler sideways and lowering it between the exhaust and frame and also using a smaller aftermarket cooler from Ultracool which is really small but also has a built-in auto fan.
The stock saddle is not that thin. We have had Corbin make thin, thick etc seats. But again, without knowing your inseam Tony's advice is spot on. Corbin can take the stock pan and work wonders on it.
We have another client who is smaller framed and he had a boot maker add height to his riding boots
So there are many options just what do you want to give up and what do you want to spend?