hmm...I would consider oversized JDM ITR pistons, your rods are fine, upgraded valvetrain with either OEM "CTR/ITR", Toda, Buddy Club, Jun cams. AEBS intake manifold since it produces a tad more than the skunk2/ITR, and for sure convert to OBD1 and run a Kenji spec ITR maps.
intake - your choice but i always recommend either the IceBox , or Faux J's Sausage
header - hmm....Toda, SMSP, HyTech, HeaderTech, AN-R...bare minimum would be the JDM ITR 4-1 Header.
good luck.