There is a fonts tab on the properties panel. Raster fonts generally work better than TrueType fonts, mostly because they are fixed-pitch (as Dos was). Changing the font size just alters the size of the window, it cannot be resized manually in the enlarge directions, but can be dragged to a smaller size, in which case you should get scroll buttons right and/or bottom.
Then the size tab should have both screen buffer size and window size as 80 wide, 25 high. Anything other than that could easily fool some old Dos programs which assume the screen buffer MUST be 80x25 (and why wouldn't it be ?)
You get full size by keying Alt-enter back-and-forth. As jmmd says, in full screeen any misalignment is down to the monitor. Any misalignemt in an actual window smaller than your monitor size would be something I have never seen. Having said that, there are loads of ways in which a dos window is more than oddly behaved in any OS later than win98.
You must tell me what OS you are running under, and comment on the full-size/windowed points made above.
In Doom "DOS gamesonline" the screen inside the window can be "narrowed or widened" by use of the keyboard (-) and (+) keys as opposed to the number-pad-keys