Done an H/C/I and got car running..but seems low on power?

I have a 91 5.0 that I recently finished putting a B303 cam, GT-40 Iron heads, and Explorer GT-40 upper and lower intake on. Got the car all together and it fired right up. So the car had a slight miss to it, and knowing me, using the old plugs that were shipped with the heads, one of the spark plugs was actually arcing on the outside against the head. So I replaced the plugs and it got rid of most of my problem.

I took the car out for a spin today and whenever I floored it, it just seemed like it didn't have much power, and other times I floored it she really picks up and plants me back in my seat. So I get home and I pull off the vaccum hose to the FPR and I got no vaccum. Not even any vaccum out of the nipple on the intake. Same for another vaccum line that I checked. So I put them both on different nipples which had very good vaccum, readjusted my fuel pressure and I took it for another spin. It did seem to run better but still seemed down on power yet.

Also I noticed that when I'm coming up to a stop sign and push the clutch in, the idle surges about 2 or 3 times then it idles nice and smooth at about 700 RPM. The car also has a little hesitation when I feather the throttle. I think my car is running a little rich or just starving for more air. Maybe something electronically, I don't know.

So here is some info on the car and what I have done to it:
-The timing is advanced about 10 degrees with the spout plugged in, should I take this up some more? I put 93 octane in it today.
-I moved the Air Temperature sensor to my cold air intake tube, about 6 inches before the throttle body, since the lower intake did not have a location for it.
-The engine does not smoke or make any kind of noise, although I do have an exhaust leak from where the headers butt up to the H pipe on both sides, I'm going to drop the H pipe again anyways when I do some tranny work.
-I have the fuel pressure set about 38 or 39 pounds.
-I have the stock fuel pump and the stock injectors on it for right now. I would have upgraded but I'm a college kid on a budget lol
-The exhaust does cackle and pop sometimes when I rev it in the driveway, I even heard it backfire twice.
-The throttle body and mass air meter are the stock ones as far as I know.
-Before I changed the plugs I seen the cat glowing on the same side as the bad plug, but I did not see it today.

I am glad I went with the setup I did. It was cheap and the B cam sounds wicked. I would like to get this engine straighted around before I drop the rear to get 3.73's in it...lol
Any help is appreciated.
Thanks.

Thanks. I do have high flow cats on the car. One thing I will definately check is the vaccum issue. And I am wondering that if a lower intake gasket is leaking, if air could possibly leak to another cylinder and cause it to run poorly. I don't know, but I am going to test my vaccum this morning and maybe even bump up my timing a few more degrees.

And the thing with the electronics is that I do not have a check engine light on. Before I done the H/C/I, I was having problems with the EGR valve. I got either code 33 or 34 I believe, and just basically ignored it because I knew I was going to build it up some anyways, and the car ran fine.

I'm going to try unplugging various sensors and see if anything there helps out. I had a bad MAF on my ranger one time, and it didn't throw a code until it started missing and really running like crap. I had very bad pinging too.

Thanks for your help, I am going to go try a few things.

yeah, I was thinking though that if I unplug it the computer will go into a loop and give it a set value, or in other words known as "limp mode". It may or may not help me out but I am going to try anyways.
Thanks.