To delete the EGR, you just pull the valve assembly off and plug the holes in the exhaust and the intake. Then you have to disconnect the electronic part and disable it in the tune. As for HP gain? I don't think so. From what I've read, deleting actually hurts mpg but I have no visible proof of that yet and this is the first I've deleted it with. It's a 63 and in this state, it's not an issue. If I were going into a Fox, I think I'd keep it. I'm going for the minimal clean look here.
These engines are said to respond real well to boost due to the high flow characteristics of the heads. The problem is, your lower end(mine too) is limited to around 450-500hp. The crank is a 6 bolt but will still be fine. The rods and pistons are said to be the problem. I am getting mine running and setup to go and then pulling it all to paint the car and forge the bottom end this winter. There is only one aftermarket intake for these that I know of and it's stupid expensive and not usable down low in the RPM's. The MMR intake which is what the guy I bought my Cobra intake off of is using, he's going twins on his setup and will need it. The Cobra intake is had cheap enough and can be ported for good gains. I have 3/4" shorter runners in mine as well as port work and I run the MMR spacer and IMRC deletes and the Accufab 1200cfm single blade TB. That's plenty for a street or track car. There's no need to go more unless it's a dedicated high RPM track car. I almost picked up the newer Mark intake but it is said to be the worst flowing of all the intakes. Your Mark intake is great for torque and probably tops out at 5500rpm stock. Of course, boost changes that.
You really need to read up on what you want out of it. Look at my build and you'll see I change my mind......a lot! I've had a turbo setup, a nitrous setup and now a Vortech bracket on it for a blower and I just barely started it for the first time yesterday! I'm finally set on what I want and it cost me a bit to go through all that. Know your goal and search for the parts. If you can fab, you'll save tons.