Convertible top alignment issues.
 

I replaced the transmission gears on the convertible top a few months back and due to it being too hot to work in the garage, have just now got everything back together. I am having trouble with the convertible top pushrod arms colliding with the lift arms for the clamshell when the top is fully up and it knocks the convertible top arms off the ball socket (and I would suspect when it is down too but I can't confirm that yet). All the marks on the transmission case, lever arm, and drive gear match up on both sides. Any ideas where to begin?

My guess is that you have the arms on the transmission installed on the wrong sides of the car.

Check if you have the same issue as in this thread with the part that bolts onto the transmission being oriented incorrectly: https://986forum.com/forums/boxster-general-discussions/86181-convertible-top.html

The arms are on the correct sides as one has L in the part number for the left side and one has R in the part number for the right side.

The lever arms are installed in the correct orientation (like a frown).

Can you post pictures of the transmissions when the top is in service mode?

I will try to get some photos eventually. I just looked at it again as I had the drive cable come out of the sheathing on the driver side transmission and low and behold now the lever arm on that side somehow wedged itself under the sheetmetal right below the track that the clamshell rides on and bent at least one of the transmission studs that mount to the body pretty good. The transmission I was able to remove and it still works but the entire cable sheathing seems to disconnect from the transmission with no effort which is a bit troubling so I may just end up buying another transmission assembly for that side. I am hoping I can put a 13mm nut on the bent stud(s) and bend them back to square with one another. I've spent way too many hours the past year off and on trying to fix what was a broken gearbox gear to the point I am entertaining ideas of selling the car sadly.

The cable should click in so either it isn't fully seated or the plastic retaining clip has been snapped off. I sheared one of those fasteners when going to tighten it. Not the best metal so my guess is you won't be able to bend it back - good news is they aren't that expensive to purchase.

I was able to get the transmission mostly aligned properly again but I still feel it is slightly angled to the body side compared to what it was originally. I got the cable back in and the two transmission aligned again with each other but just haven't had time to look at it again and it may be the weekend before I get too. I am not familiar with the plastic retaining clip you were referring to unless it is the clip that holds it into the motor assembly in the center in which mine are brass and are doing their job.