The 3 bolt necks on the CBS-era strats were flawed by design. There was a reason that Leo Fender designed them with 4 bolts...
Commonly what happens with these necks is the holes drilled through the neck get wollered out from the movement of the neck because there isn't a proper amount of anchor to stop the neck from moving slightly as you do heavy vibrato and bends and such. Many of these guitars, like CSchlegels have been converted to a 4 bolt guitar to fix the issue... HOWEVER, being a Fender purist... I don't recommend doing this unless you're ABSOLUTELY set on destroying the historical integrity of the guitar.
If drilling out the holes and filling them with dowel rod, and redrilling them did not work... You're only other option may be to look into installing some threaded inserts. This will keep the wood from stripping out around the screws and may give you a more solid joint between the neck and body... might even increase resonance. That's the importance of a tight neck pocket anyway!