Changing the motor to something else will add more weight and also take away the 'flavour' of the KLX but each to their own.
I also blew a gearbox with a 290 kit but to be fair I was doing a lot of flat shifting (holding the throttle wide open & flicking the clutch while changing gear)
It was a vain attempt to get that surge in order to keep up with a mate on his YZ 490
Have a KLX project of my own and was going to have a 'play' with the internals again, keep thinking I have more resources and knowledge now and I can do it "properly'
If I really had more knowledge though I would leave well enough alone!
One thought I had was to fit a cush drive rear wheel which is usually better for the box but Leith got me thinking the other day about cush drive clutch hubs.
Not sure if the KLX had one of these but I know my 89 KX 250 did as the rubbers disintegrated in it causing all manner of fearful noises