How do you tell what year the transmission is on a Samurai?

I ask because I have a '90 Samurai and the transition shifter locating bolt is the smaller one...I read where '90 trannys and later have the larger locator bolt...

Also when I pulled the motor and transmission I noticed the "rod thing sticking out front of tranny" is really wobbly and moves back and forth...I was thinking that's not normal bc the tracker tranny I pulled with similar mileage was a lot tighter

Right.  Normally, the 90 and up trannys have the larger shifter locating bolt.  But that doesn't mean someone didn't swap the shift tower and shifter out for an older one (they directly interchange).  Or it could be that the tranny was swapped out at some point....afterall, most of the samurais are around 20 years old and a lot of things can happen in 20 years.
What most people want to know is what 5th gear ratio the tranny has.  That is easy to tell, by looking at the fill and drain plugs on the tranny.  A tranny with square drive plugs has the later (88.5 and up) ratio (.865) and one with the hex headed plugs has the earlier (86-88) ratio (.795).