Was the paint consistant on runs of Fs?

In a one word answer,,,,,NO!  EMD had a VERY close working relationship with Dupont, Rinsed-Mason, and Sherwin Williams, such that one customer;s styling and painting requirements from one order to the next, simply did not change, UNLESS the customer made changes.

Even if they had tried to match original paint, I doubt the 1st run would have matched up due to weathering.  Some of Seaboard Air Line's units started fading pretty quickly in the summer sun down south.

Not an F unit, but I've seen an E7 that looked to have been painted with a brush:

In 1985 or '86, I was sent to EMD for a week of training.  While I was there, I gained permission to go over to the paint booth, where they were painting new CalTrain F40P's. I engaged the paint crew in conversation about this very subject.  They showed me the official drafted patterns, which were produced on an Ozalid machine and were used to make the stencils which, in turn, were used to mask the design, and this included the numbers in the number boards.  They gave the locomotive an automotive-quality paint job. 

Railroads usually wanted only specific colors of paint for specific circumstances, and would give the builder the serial numbers from the paint manufacturer as to what specific color they wanted with diagrams of where exactly each color was applied.

I have read in the KEYSTONE that the PRR did have SOME color drift issues on paint of the same color, even it it did come from the same company.  But because they used what they had, and with weathering, it was not a major concern.  Seems it is more of a concern to the fans and modelers.  Modern paint dies of today seem to be more stable.

EMD's paint chips were a big help for the NS Heritage project