I took my Pista (a 2005) out for a ride today and noticed that there was some play in the headset so I went home and adjusted it...

... so I know you aren't supposed to overtighten the stem cap bolt, but if I only slightly tighten it I get play in the headset...

So I tightened it pretty good, until there was no play at all... the bolt was pretty much threaded all the way in until it was tight... I can still turn the handlebars freely...

Is there any problem with this? At least there's no play in the headset now right?

if your headset is spinning smoothly without play, then you should be aces.

I had to do the same thing. I just loosened the pinch bolts on the stem slightly and tightened the top bolt down slowely until i lost the play in the head set, then torqued the pinch bolts back down.

You did it the right way.

you loosened the stem first, right?
if so, then you're gold.