Whenever you loosen or take off the strings, the tension is also relaxed causing the neck to bow due to the lack of the string tension pulling it flat. Do your measurements with strings on and tuned. Figure your needed adjustments like that. Then make the need adjustments, particularly the truss adjustment, with the stings very loose so as to not influence the straightness of the neck. Then retune and see where you're at with it. Series of trial and error in getting the sweet spot. Always get the neck to the proper adjustment, then adjust string height with the bridge/saddle adjustments.
If your bass was to your liking before you "messed" with it, try and recreate that same situation again. Then read and watch the several articles and videos that are available here and other places on how to make adjustments. Also be aware that string size will sometimes influence the setup too.