That 3.910 plate is referencing the flow bench they used to come up with their cfm numbers at a given lift.
If the only reason you are boring is to fit larger valves you might not even need to bore if your block checks out. I would still replace the pistons with that many miles but the rest might be good yet. Pick up a good used set of 243/799 heads and run them or have them ported and run the stock bore. FYI 799 heads come stock on many gen 4 5.3's.
http://ls1tech.com/forums/ is a good source for used parts and info specific to ls stuff, not sure if you have been over there yet.
Before you buy or bore anything I would check things over and then call or email whichever company you use and lay out your plan and have them make some suggestions as well. Maybe your stock heads can be worked over, they will be able to tell you. When I bought my cam package it helped me make some decisions on lsa and lift. I bought my stuff from Texas Speed, but there are other places too.
Couple more links for you.
General Head info
http://www.performancetrucks.net/for...g-info-434396/
This one has a stage one more suited for a stock bore, and stage 2 for ls1 bore
http://www.totalengineairflow.com/cu...gm-2/5-3-gm-ls
Set of ported 243/799 heads
https://www.texas-speed.com/p-1391-p...ted-heads.aspx