I'm noticing on all these manifold there is a TB plate just slapped on a plenum - does anyone taper these two together? You're going to get massive vortex action inhibiting flow in these areas. Granted it was a restricted engine, but we had a 20mm restrictor tapering over about 5" to ~40mm that increased airflow by 15% just by adjusting the taper from 5* to 7*, but then lost 20% from 7* to 9* because the airflow started separating from the wall and became turbulent. Just some more food for thought. The injector 'nubs' are there to create a little turbulence for better fuel mixing, mainly at low RPM's. If it's a top-end all out motor, then grinding them out for airflow is better, but for a street engine you'll gain MPG and low end power if you keep them there. New engines employ a device that uses a small cam to rotate into the intake runner at low RPM's to do this, and open up at high RPM's to increase flow.

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'95 GS w/ t3/t4b
FMIC, diy piping & RFL BOV
MS2-Extra Fuel&Spark
50 lb/hr Holley injectors w/ 1:1 RRFPR
JE 8.8:1 dish w/ Hastings Rings
Eagle Rods w/ ARP bolts
ARP Head studs
Mild port/polish head
3" custom DP/cat section, 3" PIT catback
dual MBC - 12 psi / 20psi