alpha one shift shaft alignment issue

hey there., so i have this gen 1 drive with a shift shaft that when in forward is off by about 1/8-1/4 inch. it just does not line up with the front stud. it is not a full tooth off.
you would think this would not be an issue and you can make up the difference in the linkage but that shaft lever is so wide, it has no wiggle room and installing the drive was a freaking nightmare, i was under the boat lining it up with the receiver while on other guy pushed the drive in then i proceeded to spend the entire summer making adjustments to see if i could make shifting easier . finally i said , deal with it till the boat comes out of the water and we will address it then., so now its on the bench and i have tried replacing the lever thinking maybe it is bent but
i have another lower section and it lines up perfectly with the stud. and the lever from either unit lines up .
does the shaft that goes down into the gears have finer teeth that it could be off down there or is it as course as the upper part?
does anyone have any other thoughts on why this would be off like this ?

this is the unit that is not lining up.



and this is the unit that is lining up

in the pics are both lower units in full fwd gear?
Remove the brass shoe, turn the shaft fully clockwise and then set it back on. if not at 12:00 or if past 12"00 then the "C" selector may be damaged or the shift spool is badly worn showing the shift arm going past the 12:00 position

yes , both are in full forward and it is not going to 12:00. thats the issue, it wont go full straight on with the stud.
i have tried 3 different shoes and they all land at the same spot yet line up perfectly on the other lower (#2)

To me it looks like the stainless shaft is bent.