Engine Problem

Hello, My Explorer recently had the Upper Intake Manifold Gasket replaced. It runs much better than it did. We were told that the Lower was fine and did not need to be replaced. Before it used to rev up between 1st and 2nd gears especially with the ac on. It would do it every now and then without it. We replaced the battery in it and it didnt rev up as often. Recently after fixing the Gasket it reved up again only once just like it did before we replaced the Gasket. The alternator bearings are making a lot of noise. The Check Engine light is off now too. What could be the problem and can it get worse?