I just went through this with my 89 CR500. I used the All Balls conversion bearings to adapt a complete 03 CR250 front end on the 500. Custom valving and springs though Over The Top Motorsports. He also did the work to adapt a 96 125 shock on there, along with valving and springs too.
In your case the stock 500 shock is a modern design with adjustable high and low speed compression damping. Have it sprung and valved and you're good to go. The 46mm front end can be sprung and valved to work well, but fitting a newer front end results in better forks, brakes, etc.
For your 02, just have it sprung and valved for you. There's nothing wrong with the factory stuff, simply updating and refreshing the boingers will have you happy.