My advice would be... try not to use Bootstrap. Why? Because bootstrap has predetermined classes and styles, that are the ones probably making your life imposible at the time of PSD translation. Try to make the grid once in a while, when you understand the logic behind a grid, you'll know when Bootstrap is useful and when is going to be a pain in the azz.
As @mgiambanco said, Practice, practice and practice... and when you've finished practicing, practice a bit more. Try learning from places like tutsplus, leveluptutorials, lynda.com, etc.
And to answer your problem, you didn't had to change the position nor top to make the border disappear, you could've just change the border size to 0 or make it transparent when :hover or :focus is on.
Rodrigo Garcia
Ninja man