The way I jetted my wife's 86 lt250r was run and if it flattened out on the top end I would go up a size on the main and would ruin it again and did this until it started to bog then backed it down one size.would that be the correct way or at least a good way to get the right jetting.

Jetting is a trial and error routine.  I would have started with it so rich that it misses near the peak Rpm in the first few gears.  Then lean it down a main jet size at a time until it starts pulling through the first few gears without any miss-fire.

If you stop at the point where one jet miss-fires and the next leaner jet does not miss-fire you will not be at peak performance but will be at a safe main jet size. 

If you want to tune it for max power you will need to find a way to gauge your acceleration by comparing it to another bike with similar power and do some roll on side by side acceleration runs with different main jets.  Or you could use a dyno that can put enough load on the engine so that it takes 5 to 10 seconds for it to pull through the RPM range.  You can also use a stop watch, drag strip etc. to gauge your performance with different main jets.