Don't feel bad, when it comes to tubing and plumbing it can get very confusing as to when they are talking about I.D. or O.D. because they don't always specify and just assume your application is the same as theirs. When it comes to NPT threads they are refering to the inside diameter of the pipe the threaded end is intended to mate with, and the O.D. of a 1/4" NPT thread is about 1/2". You can buy connectors that have 1/4" NPT on one side and a barbed connector on the other side that will fit most any size I.D. tubing. Most places that sell plumbing supplies will have these type of connectors. What I often do is take the old fitting with me to Home Depot and a short piece of the tubing and look for a connector what will connect one to the other. This way you have them with you to compare, or to show someone else who offers to help you.
As for your flow rate gauge, it is fairly useless and unnecessary for our application as your flow rate will probably be way too low to even register on it which is why most hobbiests measure their flow rate in bubbles per minute which is not terribly exact, but it doesn't need to be an exact accurate measurement just a consistant one.