Here's a couple pics you can see this is a big project for someone who has ridden much less worked on one of these things and forgive me for thinking that this was the place that you went while making those mistakes. I'll just stick with hands on learning process
Aside from the motor, what other "issues" are you facing? That looks like an F4 swing arm as well, which I would have to guess by it's set up will not work. The linkages and mounts for the 900 are very different. Was that swing arm on it when you got it?
To save you a lot of time, you might want to seriously consider selling the 600 motor and finding a 900 motor. The sub-frame is also hacked up but, I'm guessing that's because of the 929 looking tail section.
You have a lot of work there, we aren't very familiar will such modifications that you're presenting. While we have years and tears of riding experience and some "typical" mod experience, there just isn't enough traffic on this site with custom work like you plan on doing.
There is one thread here, but I don't know if the pictures are still view-able. He put the 1k motor in his 900 frame, with massive frame cutting, welding, and removal of the coil cross beam.
He has a YouTube channel now, and can shed some light on what you may need to do with the 600 motor.