It looks like the far end was built into a corner. If so, were heavy duty lags used to screw into the studs along that side wall as well? And is the opposite side also built into a corner and properly secured?
If so, then I don't think there's much cause for concern. The creaking is probably the 2x4 you added rubbing against the 2x6 you secured it to. You may want to consider adding a heavy duty mending plate across the front reduce movement.
If the sides are not secured to the side walls, then you definitely want to either secure them directly or just run another 2x4 or 2x6 beneath them and lag that to the wall studs.
Looks like a well built unit though, so you should be able to use your pull up bar with only making some minor improvements.
If you want some extra piece of mind, you could always pick up a couple adjustable floor jacks and place one on each side of your pull up bar so that there's more direct support towards the front/center of the shelf, which is the weakest area of it.
Hope that was helpful.