Think I got to the bottom of this today.
Steps followed.
1) Put the top up as far as it would go with motors (as in pics in first post)
2) Removed interior side covers so that I could see the gear arms and limit switching.
3) Loosened the bolts used to manualize the top. I did not turn these out even close to 4 full turns as manual suggests for 'emergency operation'. Just used a ratchet wrench to loosen enough to free up the arms. Note that the top would not move freely as a manual at this point - bolts not loose enough.
4) Now that the tension was released I was able to close the top fully and lock it.
5) Tigthened the bolts up
6) Unlocked and raised and lowered the top several times with motor. After a few cycles the top would not close fully as before.
Looks like the issue is that the bolt on the driver side is not staying tight and the arms come out of alignment. The manual says to replace these once the top is operated as manual. So I am guessing that a PO went manual, did not replace the bolts, and motorized for sale. Should be a simple fix to replace, but since I can't see where the bolts are seating in the worm gear mechanism I am going to have a local P mechanic replace them when I get some other items addressed.
Thanks for the help. Both the sealer manaul and the s2 top manual were very helpful.