Your thrust shaft isn't
that much out of alignment. Mine isn't exactly centered either. Looks like your clutch has been apart before based on the screw heads and I believe I only see one flex spring where 149's should have came with two. No biggie there, just noticed... Anyway, also make sure that your PTO handle is tight against the rear of the handle bracket when it's in the 'disengage' position. I have a early build 149 like yours, and I had a bear of a time getting the engage/disengage right until I saw Diz Jr's trick with the wedge (his is a fancy steel wedge, but wood works for those of us who don't have access to a foundry
). The little notch that the pin sits in at the base of the handle will egg out over time and cause the PTO not to disengege fully. We're talking about a game of inches here, specifically a 1/2 to 3/4" of movement being all you need for that thrust arm to do it's thing.
Nice pickup on the 149. Mine originally came with the 48" QA deck like yours; I've since upgraded to the 'A' style deck and mule drive. The 1x8/9 series are some of the stoutest Cubs made IMHO and are easy to work on, too. I've had 3 or 4 149's, a 109, and a 129, all well-built, with lots of options for mower decks...
PS- It's also possible that your entire engine 'could' be out of alignment if the 4 mounting bolts are loose or missing... The thrust arm is pinned in laterally, so unless it got bent somehow, it should not be the problem. Again, not a major misalignment, all it will do it wear the carbon button on the one side.