Just put em on the bridge and intonate. Don't bother measuring, that only needs to be done when placing a bridge onto a virgin body. It's nowhere near accurate enough for correct intonation.

I would check the neck alignment, adjust the pins on the saddle to 4/64 and intonate. I have this happen frequently and this works well.

How do I check neck alignment?

For the sake of this explanation, I will have to presume that the angle of the neck as it sits in the body pocket is within an acceptable parameter.

Ensure that the outer strings as they leave the nut and travel down the neck are at a uniform, parallel distance with the edges of the neck and that the D and G strings are likewise with the position indicators. If they aren't, you may have to shift the neck in its pocket ever so slightly left or right to make this happen. If you do have to shift the neck, "tweak" tighten the neck plate screws immediately upon satisfactory completion of the shift. Do NOT tighten them for, "dear life".

Next, well the way I do it is 'the old fashioned way', long before capos, rulers and calipers were thrown into the mix and "Infallible Web Dogma" evolved many a
bloated 'scientific' dissertation on the, "end all of end all" ways of how to 'perfectly' do it. Many might disagree with my method but for 43 years now, I've never had any complaints nor malfunctions:

Make sure that your guitar is in tune first. If (hypothetically) your normal way of playing is with the guitar tuned a whole step down, indeed, do tune the guitar this way. Having accomplished this, simply pick up your guitar by the body and point the neck forward away from you. Turn the guitar to approximately a 160 degree angle, holding it at eye level on the right side of your body. Now, make believe the bass side of your guitar's neck edge is the top of a rifle. The highest fret is your rear sight and the first fret is your forward sight. Essentially, you will be zeroing in on the edges of the frets and the frets' low E string area. Start aiming. Keep looking until you have the last and first frets synchronized just like you would a rifle's sights. At this point, you'll be able to see clearly any bevel, arch and/or twist in the neck and can take appropriate action. If the neck is bowed, tighten the truss rod a quarter of a turn at a time; sight the neck again and keep repeating the tightening/sighting as necessary, reducing your turning increments of the truss rod until the neck is ALMOST perfectly straight. You DO want the tiniest of a bow to remain there. If the neck is arched, do the opposite to the point of where you've introduced the tiniest of a bow. If the neck has a twist in it, well, we'll take that one as it comes (if necessary).

The reason for the tiny bow is because if the neck was perfectly straight, the wound strings would rattle off the frets below them.

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Thank you so much!!

Any time!

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