Hey flyride,
I actually got my car back together last night so I thought I'd get back to you. The idea to tape around the threads on the pushrods and install the new ones at the same place didn't work with the metal ends because they don't screw down as far as the plastic ones did. What I did was screw them down until they bottomed and then backed them off about a quarter turn until the sockets were facing in the right direction (about eight threads were showing). Then I stood the pushrods up and measured them to make certain they were exactly the same height (they're adjustable).
Now let me try to explain what I did next, because I think it may be your problem...
I timed the transmissions to be at the exact same place at the exact same time. To do this, you'll have to disconnect all of the pushrods from the transmissions, both the top pushers and the boot pushers. REMEMBER WHAT POSITIONS THE Vs (legs on the transmission that operate the pushers) WERE IN AND WHAT POSITION THE TOP AND BOOT WERE IN WHEN YOU STARTED!!! If you get it back together upside down, the top will cycle backwards. Don't ask me how I know this.
With everything disconnected, run the top motor until one of the the legs of the V is parallel to the floor. Get it exactly level using a ball level. Keep bumping the top motor until you have it perfect. Now go to the other side of the car and check the other side. If the leg on the other side is perfectly level also, you're good to go. If not, disconnect the cable from the motor and use an electric drill to spin the cable until that leg is perfectly level as well.
Once both sides are parallel, the transmissions are perfectly timed. Run the top motor until the transmissions are back where you started and re-assemble everything.
This procedure is a little hard to explain, but it wasn't hard to do...trust me.
