A systematic set of exercises can help. Try to practice every possible move in isolation. Do these at each fret position to get comfortable all over the neck.
Index-Ring, Middle Pinky.
$6 1 3 $5 1 3 $4 1 3 $3 1 3 $2 1 3 $1 1 3 2 4 $2 2 4 $3 2 4 $4 2 4 $5 2 4 $6 2 4
The "spider" (can be mirrored 4 ways):
$6 1 2 $5 1 $6 3 $5 2 $4 1 $6 4 $5 3 $4 2 $3 1 $5 4 $4 3 $3 2 $2 1 $4 4 $3 3 $2 2 $1 1 $3 4 $2 3 $1 2 $2 4 $1 3 4
Buddy Holly riff (do it with Index-Middle/Index-Pinky and Index-Middle/Index-Ring).
$5.1.$4.3 $5.1.$4.3 $5.1.$4.5 $5.1.$4.3 $5.1.$4.3 $5.1.$4.3 $5.1.$4.5 $5.1.$4.3
Drop D Power Chord Scales. Play with Index Barre, Middle Barre, Pinky Barre, and shift up to higher positions. You want to be able to go up and down each string as well as across all 6.
$6.0.$5.0.$4.0 $6.2.$5.2.$4.2 $6.3.$5.3.$4.3 $6.5.$5.5.$4.5 $6.6.$5.6.$4.6 $6.7.$5.7.$4.7
Search for "The Steve Vai 10 Hour Workout" for a really excellent set of exercises.