Firstly let me congratulate you on basically unworn ways - this machine is in great shape! If you were to put an indicator on the Y saddle way and indicate the Z axis way at the discolouration, you would probably find a couple of tenths of deviation where the discolouration occurs... Certainly nothing to be worried about. Your Y ways are in perfect shape. You can view one side of your X ways to check by running the table to each end, photographing the ways from below. I would guess that they are in good shape, except for some corrosion as per the Z ways. The discolouration is very likely due to the machine sitting idle and un-lubed for years, so that condensation collected could erode the z way at the point of contact. No biggie.
A Quick warning: I'd stop using steel wool and move to a stiff plastic brush or a plastic pot scrubber. Firstly, the steel wool cuts the cast iron. This produces micro fine particles that are hard to get rid of and contaminates the oil in your ways. Secondly, steel wool is fairly aggressive and I'd not want to round off any of the flaking (scraping marks) out, because they hold oil, which ensures the life of your ways. Oh - and thirdly, a fiber of the steel wool can fall off, remain unnoticed and get in between the ways, scoring them for posterity.
A way to get rid of the iron oxide is to do spot application of CLR and then rinse and re-lube immediately. Paper wipes, followed by Alcohol and / or WD 40 are helpful in purging the water before rubbing on way lube... It is important to get rid of all the water before coating the ways in oil.
From your description, I'm guessing that you were talking about measuring in X. I would repeat the same indicator check in each of X, Y, and X, and record the results. Now to your problem: What you are seeing is not uncommon in older machines, where the ways in X are worn in the centre of the table. To fix the ways will tale a lot of work, and completely disassembling the components of the X and Y travel [If you have the table off it makes sense to do both.] In the majority of cases, the Z travel isn't far off or worn enough to take the knee off - a very big, heavy job...
You could disassemble the table by following the steps in various Bridgeport maintenance manual (there are a few fiddly bits, and its too long for my memory...) If you are interested in very light use for the moment, why not just lube up , and start to use it, gain confidence, then do a complete rebuild when you have 'more meat in the game'?
(Or, if you don't like I could buy it from you! - Just kidding)