How do you secure hooks in hand made balsa crankbaits? I have got some I  made that I used epoxy to glue in 3/4" screw eyes. It seems that such a light wood any descent sized fish would be able to pull the screw eyes right out of the balsa.

Lure making sites out here in the www.  try tackleunderground.

Sounds like your basic approach is sound with the epoxy and screw eyes.  Only improvement i can suggest is reference to West Systems epoxy

http://www.gougeon.com/

for the properties of various filler additives.  This is expensive way to go and may not be justified.  I never used balsa wood,  some makers use basswood, cedar, or straight grained pine.  They use a wire harness system which is glued into a split blank.

One idea - which is used on some Japanese trout swimbaits I have -  is to use heavy braid (Spectra or PowerPro) as the harness and connect your hooks with split rings.