In the pictures I posted the two Al boxes on the original panel are the RPM transducer and a rear window defrost relay. I am not 100% sure if they are used.
You were also asking about a flat 5 pin connector - maybe the one shown below by the dist cap. It is not used in my set up nor is a small round 3 pin connector.
By the way... if you still have the engine out and have not yet done so, check the fuel lines. The 3.2L have three lines which are known weak points and are a PITA to replace with the engine in the car .... ask me how I know .
(there is another recent thread where I have received several good reference threads on this issue.)