Joe is correct that many, if not most, 4-4-0's had the main rods inboard of the side rods.  I believe PRR 1223 at Strasburg is this way as well.  If you want to "correct" it, it should not be a big deal.  You'll need to get a longer crankpin screw for the rear driver (probably the same screw as the front driver crankpin) and then find a piece of brass tube or small washers to bush out the side rod to keep it square to the crankpin. 

The "early" Bachmann 4-4-0 represents a fairly typcial engine from about the mid-1880's to about 1910.  If you want to backdate it some, as noted you can replace the domes with earlier style "ringed" domes, add a big oil headlight, and a capped or diamond stack.  It already comes with a wood panel cab.  You might wait to see if someone like Banta might do a replacment cab with a peaked instead of round roof.  It won't take you quite back to the 1860's-'70's period, because back then the firebox was still placed down between the frame members, leaving the boiler sitting quite low.  The V&T locos are in this group.