I do believe it would be easier if the lower pieces went in first as the seal fits on top. Probably not mandatory, but helpful. As Hans says, please use the MB seal. It is an extremely complicated extrusion profile and will be the difference between success and failure.
I recall that both the upper dash pieces and the upper windshield frame wood bows rest on the windshield seal. Therefore, they have to go on after the windshield is in place. I will check on that further.
Concerning the caulk found below the seal. I do now believe that it is original indeed. The reason is because of the chrome A pillar trim. Long story short, I had to remove that A pillar trim piece and chrome it before I reinstall the windshield. Why? I wanted to chrome it later, but it CANNOT be removed without the seal coming out. See 1st pic (4433). There are three hidden screws behind the seal. Shown is the bottom one. I am not going to remove the windshield seal again, so it has to be done now.
Ok. When I removed the trim, there were three places below the A pillar trim coinciding with the screws that had the same caulk (color and texture) that was below the windshield seal. That trim piece has never been off. Therefore in my opinion, the seal caulk is factory Mercedes. Next picture shows caulk on the headliner. PITA to get off. Final pic is the operation to remove the caulk. What a job!