I am no expert, but I agree with Guitar Dad that Jamie Andreas' book provides an excellent approach on how to practice. I found some of the drills in the book to be very practical and helpful. Others are kind of out there, but I suppose they are useful. His main message is to relax and play accurately. The drills are designed to achieve those goals.
I think the main solution to your concern is to slow everything way down and use a metronome. Play scales and other drills precisely and it will translate into your playing pieces precisely. The only way to learn to play precisely is to slow it way down and only increase the speed when it gets easy at the slower speed.
I can not remember exactly where I read it, but it was a classical guitar instruction book. The author states that she learns a new piece by playing extremely slowly- for example sets the metronome at 60 beats per minute and plays one note every four beats! Once it is smooth at that speed, she keeps increasing the speed until she is playing at concert speed. Accuarately timing the picking finger and fretting finger is the key to playing accurately and smoothly and that must be ingrained at slow speeds.
