The timing cover hole is for the oil hose that connects the lower outlet on the oil filter to the timing cover. If yours is plugged, it's likely that you don't have an oil filter on this engine.
A properly functioning heat riser and damper system work well to improve cold starts. If you don't want to get it working, make sure the damper is closed to the bottom of the carburator. It's unlikely to freeze back up in short order. It probably took 30-40 years...and no maintenance for it to freeze up the first time.
The plugged ports on the intake manifold are vacuum connection points. They should remain plugged if you won't be using an original vacuum wiper motor.
Tim