1993 Toyota Pickup SR4 3vze Auto Rough Idle / Stalling low RPM

I have a 1993 Toyota pickup with the 3.0 automatic and sitting at 248K, the head gasket went out a month ago. I tore it down replace the head gasket rebuild the heads also added some headers to get rid of the cross over pipe. While I was there the rusty EGR bolts broke so I deleted the EGR, capped my vacuum hoses and smoke tested. The truck runs pretty smooth driving down the road maybe a little hesitation but barely noticeable, but at low rpms it lops like a cam and sometimes even stalls. I've checked timing, maf sensor, oxygen sensor, idle air control valve. My only conclusion is I pulled each wire to the distributor cap my results the rpm changed on every coil but 1 and 3 did not change as much as the rest (I replaced my wires, plugs and injectors).