TIMING MARKS ON B2000 A versus B or C

I have a brainteaser for someone out there I recently bought a remanufactured 1998cc engine and dropped it in. just to get things dialed in I took it to my mech buddy.It was'nt running bad as a matter of fact it ran pretty good, however idle was'nt smooth it jumped around from 800-1100rpm so he found it only had 9lbs of vacum at the intake instead of 18 which he says it should have , he stated it might be the cam timing being off. when I talked to the mec who put it together he stated the timing gear on top was alinged to the B marking from the remanufacturer and he changed the gear to the A mark #1 whats the difference between A and B ? #2 why would the factory set it up on B ?

I'm not entirely sure about the older 2.0 liter engines that have that timing setup but I believe it doesn't matter a whole lot which number the cam sprocket is installed on as long as the number it is installed in on the cam dowl lines up with the mark on the housing. Sort of like this:

http://www.mazdatruckin.com/B2200/TimeCheck/CamCenter.jpg

See how the hole for the dowl in the cam lines up with the number and the arrow at the top. Yours should be similar.