League totals are really complicated because they interact with the talent level in the league to create results. So even when you get them "right" your output will change as the ratings in the league drift. At the end of the day, I'd be surprised if there's an air-tight way to get exactly what you want. Mostly, you kind of tweak things until they're close enough for your patience.
But, if you've getting too many homers, just adjust the total up or the modifier down a little and you'll probably get it about right overall.
Note that individual home runs may still not be distributed to your desire. That's going to depend on ratings and rating distribution to some degree.
I wish there were an easier answer.