Jess --
My Jamar looks like this picture (Notice the linkage for rotation is diagonal rather than like yours which is straight up&down vertical). I have a standard VW shifter mechanism in the cockpit.
You say that it was working at one time. So, for starters you have an unusual shifting pattern or you have a different shifter mechanism in the cockpit.
Drop the long shaft from the cockpit to the Jamar off the bottom of the Jamar (it's an Allen socket head bolt on the bottom tip of the Jamar). You should then be able to grab the Jamar and manually shift the transmission through all of it's gears. It sounds like what you say you are able to do this -- at least push the tail shaft of the trans in an out. You should be able to do this if there is NO fluid in the trans.
Once you know the trans clicks through all the gears with smooth mechanical "clunk", then study how much the tail shaft on the trans needs to rotate to slide into one of the 3 "gates" (R, 1&2, 3&4). You might even be able to make some reference marks on on the tail shaft and nosecone. Then hook up the long shaft from the cockpit again.
Now have someone run the shift pattern from the cockpit while you watch the Jamar. If it now does not click from gear to gear you should be able to visually determine why.
The Jamar will tolerate absolutely NO slop in the linkage (the usual cause is loose universals). ALL movement of the shifter in the cockpit must translate into movement of the Jamar.
Presuming the linkage between the cockpit and the Jamar is sound (without slop), then once the Jamar is adjusted it is a dependable and positive shifter (no matter what others may say).
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