Sounds like the issue that you’re having has everything to do with intonation. Over time, or when changing strings, the length of the string going from the saddle to the nut can be too long or short, here’s was you do:
1: tune each string to standard tuning and then go to the twelfth fret of each string (1 octave) and see if those have the same not. If the note is too sharp, the string is short and needs to be lengthened. If the note is flat, the string is too long and needs to be shortened. Pretty much every bridge does this some time or another and you use the screws on the bridge to bring saddles for each string forward or back. Let me know if this fixes it, since there are multiple different things that can cause this
happy to help!