No, you don't have to. The L & S has a plug for that line as it bypasses the T altogether. I don't know for sure about other separators, as the L & S is the only true oil separator I have purchased...
Now the driver side of the PCV system I did nothing with. As far as I have read from those that really know their stuff 'round these trucks, the pass side is the only side that was a design oversight (flaw) by Ford. The drivers side pulls filtered air from the air box into the crankcase, which is under vacuum from the passenger side that is connected to the intake. I hope that you can paint that m e n t a l picture from my description.
Glad you're doing it right from the start. You asked in the top post I quoted if there's anything else we would recommend, I myself would say since you are cleaning the IC, you will have the SC off, so there is almost no better time than that to pull the turkey pan elbow off and plug the hole in the turkey pan. This will only cost you about an extra dollar, 45 minutes and a beat up arm from reaching between the firewall and the lower intake. The dollar for the ⅛" Galvanized NPT plug.
If the motor is not modded, then stock plugs and stock gap are all that you need. Motorcraft are what I see recommended the most for stockers, and I also see a lot of people saying steer clear of the Autolites.