Hopefully you guys can help with this one!!

A few weeks ago I went to my grandpa's to change brakes, found out outer boots on both sides were ripped. So my grandpa for some reason took all the axles off at the same time and completely dismantled them. So now I noticed that when I put the axle nut on before I put the tire on, it visibly pulls the axle and "stretches" the inside boot on the passenger side.

So here are some of the symptoms I notice: The abs light is on (no big deal) and there is a shake at higher speeds (above 55mph). Oh and the axle came out of the transmission once (before new tires).

I have since bought new tires for the front (after this is when the shaking started), changed passenger side lower ball joint (before new tires), and reseated the cv axle after it came out (before new tires).

The car drove perfectly fine before the tire change and after I changed ball joint. However my concern is that my grandpa put the inside cv joint on the wrong shaft on the passenger side. Is there a longer shaft? Which side should it go on if there is?
My next step is to switch cv shafts and see if this helps.

Please help with any suggestions you can think of!