Smog Pump Removal Questions

I am in the process of restoring a 95 Cobra and after reading this post I discovered that the previous owner removed the rear crossover tube to the back of the heads and it doesn't appear they plugged the holes.
The smog pump was still on the car but in modified form.

I'm not sure why they did this but it's now gone. I've decided to remove the pump as I am not concerned about emissions.

What are the effects of having not plugged these ports on the back of the heads?
I'm chasing numerous gremlins and I need to eliminate factors. Any help would be appreciated.

 

Yes, it runs but not very well. It had a miss. It also would hesitate and pop when given throttle when cold. I was trying to chase down vacuum leaks when I learned it was missing the crossover tube. I'm not as familiar with the 5.0 as I am the 4.6 so it's a learning process.


So I noticed the tube was missing and assumed I had an uncovered smog hole at the rear of the head as people on here suggested in other posts. Well, I couldn't find any vent holes? The bolt holes are there, but no vent. It didn't make since that my cobra was different than all of yours. Then I realized that I'm assuming that my genuine vin coded cobra had its factory engine. What if the motor (or at least the heads) are replacements?


Sure enough, I check the stamp codes on the heads and it appears I have gt40p's sitting on the motor. I have the cobra intake, valve covers, even the springs and 1.7 rockers but the heads are P heads.


I still in the process of determining how far this goes. I'm wondering now if the short block and heads are both replacements and if everything else was swapped over? Who knows what cam it may have. Maybe that's why it's wasn't running just right?


I also have a steeda driveshaft spacer at the end of my drive shaft and I'm not sure why it was used.

 

It's a VIN coded real cobra. All other cobra parts are present.

 

I'm not sure I even have them. The car is in the process of being torn down so it's not running for a while anyways.

The casting stamp on the tranny says the following.

13-52-066-919

The internet says I have the following based on that casting:
85-90 Ford World Class w/plastic vent tube (also on some 84 NON-WC)

I wish I could have spotted some of this stuff when I bought it. I would have beat the price down further. Lol.