Re-tune, check the bridge height, adjust the two big screws again, tune, check, tune, etc.
It's a pain and sometimes it takes a while to get right. Just a small amount of spring length change can alter the bridge a bunch.
I just went through this on a new Ibanez Satriani JS1200CA. It was set up for 10's but I am used to 11's on my two Strats. I tried to live with the 10's through one string change, but had to go up to 11's.
Going from 10's to 11's I had to add another spring, making it four springs cause of the Floyd type trem.
My Strats have 11's but 3 springs seems to be just fine on the Fenders.
You will probably have to adjust the intonation also.
See the intonation setup video in the reference section on this web site.
see ya