The PCV line does go into the upper intake. That's even what the vacuum diagram says. Don't you have the original emissions sticker? The vacuum diagram is on there. Mine was on the cover for the coil.
With a stock intake, the PCV line would go to a T-fitting attached to the bottom side of the plenum and then the other side of the T-fitting would go to the front of the intake manifold. Essentially making the PCV connect to two places on the intake.
There were two big vacuum nipples on the front underside of the upper intake. One was for PCV and the other for the evaporative emissions canister.
On the back underside of the upper intake was a vacuum tree with one large nipple and two small nipples. The large nipple had a vacuum line connecting to the vacuum tree on the firewall (brake booster, A/C, etc).
One of the small nipples would have a vacuum line going to the FPR, and the other nipple had a vacuum line connecting it to the vacuum tree on the passenger side of the engine. That line would feed the EGR vacuum control and the thermactor vacuum controls. Lines would then come up from those vacuum controls, back to that tree and then one line going to EGR valve, and two other lines going to thermactor flow control valves.
The only other line is the one going from the throttle body to the oil filler neck.
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351W 89 Mustang GT Convertible