#1
I just have a general question, for the record I play alot of guitar but I have no clue when it comes to actual guitar setup procedures.
Now, I've had really bad intonation problem on B and thin E string for some weeks and its a floyd rose bridge. Thin E string measures 0.009 in gauge and its new strings. Im actually not sure if thats the same gauge as when I bought the guitar. So B and E is terribly flat on 12th fret, about 1/4 tone flat and the saddle is moved as far towards the neck as it can go.
Nothing I have tried seems to work, I have already adjusted the bridge so its level and straightened the tross a bit and as said changed strings.
What can I do here? No video or article I have looked at covers something like this. If I move the saddle up away from the neck the intonation becomes perfect immidiately but 1 halfstep lower than its supposed to be.
#2
Did you get a new set of strings or did you just replace the B and high E strings? Normally, bad intonation is a sign to replace the whole set.

Try re-adjusting the intonation but this time, after each adjustment, check if all the strings are perfectly in tune, not just the one you just adjusted. As with everything on a floyd, one change affects everything else.

If all else fails, I find that intonating on the 24th fret (if you have one) works just as well if not slightly better then intonating at the 12th fret.

Also, learn how to do a complete setup.Read this guide. I've found it quite helpful in the past.
#3
Have you moved the saddles forward by removing the set screw and moving it to the one closer to the neck?
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#4
The whole set of strings is changed. Tbh first I just changed B and E and then changed the rest a week later or smth.
As for the saddle yes i loosed the screw and put it in the hole closest to the neck.