The front base is allways taller than the rear base, regardless off when the barrel/rifle was made. The rear base is on the flat of the barel above the chamber closest to the reciever. This is the thin base you have. The second/front base quite a bit thicker becuase it goes forward and is installed in a position AFTER the barrel starts to taper.
The nut to tighten the rings should be on the left side. IN other words the detent for the recoil stud on the rings, is positioned towards the muzzle of the rifle.
If you in fact have #1 bases and a "V" barrel contour this should place the scope perpendicular to the bore of the rifle as long as you use Ruger or others rings of exactly the same higth.
I once installed #3 bases on a #1 and spent years getting it right finnally using two different rings from two different manufacturers. It wasn't till years later I learned what I had donewrong to start with.
The "V" barrel hasn't changed in contour since day one, 1970. The earliest "V" rifles had two sets of holes but were scaced well appart for the use of Unertl, Redfield and other LONG Target scopes, later they added the set in the middle for the use of mdern short tubed scopes.
Last set of "factory" bases bought from Ruger, this summer cost me $58, I think, and shipping
If you have the correct bases and rings and install them correctly it's a pretty fool proof system.
If you have to the bases can actual be shimmed vertically and the rings can be shimmed to change inpact horizontaly. I've only had to do this a very few times in over 100 #1s and those were with REALLY high magnification scopes that couldn't be zeroed/bore sighted without doing it due the limmited number of "clicks" in the scope. Neaarly all scopes have enough latitude to adjust to any off cneter holes in the barrel. Only when you get up around 32X and above and have 1/16" clicks do you sometimes run out of adjustment.
Second thought:
In re-reading your initial post. If your rifle is from the VERY EARLY (prior to 1975 - 1976) 70s it is possible that the center set of base holes was installed by a smith in order to not have to use a long target scope. At that time there was no "standard" spacing for the middle set as the factory wasn't doing it back then. Even if the screw holes are the correct distance apart they may be in a different position on the barrel than the factory eventually used AND built the bases for.
Buehler made a scope base specifically for the early "V" rifles that used the back set of holes plus one additional that didn't show once the base was installed. I have these on sevral EARLY "V" and infact just sent one to another shoot er this summer that didn't care about "holes" and just wanted to be able to scope his rifle and shoot it without the exspense and time involved in finding Unertl or Redfield era correct bases and scopes.
I'll dig out the mike. First thing you need to do is call Ruger and find out exactly WHEN your rifle shipped. It is possible that it shipped early enough that the center set of holes are in fact not factory and are in the incorrect position for factory bases to work.
Let us know what you find out and we'll try and help. IF it's already got extra holes, thus has lost it's "collector" value it might be easier to use the Buehler base and rings than figure out exactly what base it was originally set up for if was NOT the factory base.
Ross