You are correct in that its all in the intake and exhaust manifolds, the head has nothing to do with it. I've never looked close at a non EGR intake to see if the bung is still there and threaded but I'd check to make sure it isn't before swapping intake manifolds.

The air pump pushes air into the head through a port in the head between the manifolds. Seem to recall that non smog pump engines have a freeze plug in that port. Not sure if the machine work is there if you remove the plug.

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90 300TE 4-M
Turbo 103, T3/T04E 50 trim
T04B cover .60 AR
Stage 3 turbine .63 AR
A2W I/C, 40 LB/HR
MS2E, 60-2 Direct Coil Control
3" Exh, AEM W/B O2
Underdrive Alt. and P/S Pulleys,
Vented Rear Discs, .034 Booster.
3.07 diffs 1st Gear Start

90 300CE 104.980
Milled & ported head, 10.3:1 compression
197° intake cam w/20° advancer
Tuned CIS ECU
4° ignition advance
PCS TCM2000, built 722.6
600W networked suction fan
Sportline sway bars
V8 rear subframe, Quaife ATB 3.06 diff