You're on the right track.
Dump the "thermactor" bosses in the exhaust ports. (that's what the large protrusions are called)
Be extra cafeful around the valve guides though. If you've already got the header gaskets, try to match the exhaust ports to those gasket openings, and go in as far as you dare.
Remember, it's better to take more material off the top of the port versus the bottom.
If you're getting new guides, it would be better to do the porting while those are out.
As far as the intake side goes, just a mild port match to gasket will be sufficient. The weak side is on the exhaust, so spend you're time there.
Check the new intake as well. They aren't always in the best of shape as far as port matching either.
Are you putting all new valves in? Ford Motorsport carries the entire GT-40 valve train for a not too extreme price.
You'll get larger valves, and better material.
Are you doing the port work yourself?
Reason, for the amount that a shop would charge, you're better off going with an aftermarket head. Most of the work's done, and they're a quick bolt on. Do some checking into "porting" prices.
Another thing to consider is going to studs and guide-plates, and installing roller rockers. You'll get true 1.6 ratio, and less friction. (Plus they look cool before you put the valve covers back on)
Oh, the cam you've chosen is a good one. It has a "split" profile, meaning, the exhaust has longer duration than the intake to get all the burned up stuff out where it belongs.
Which one is it though? Don't want to go too big, or you'll lose the bottom end, and your vacuum will be awful low at idle.
One thing to consider on determining your compression ratio, is that those later model heads have huge combustion chambers, so even milling off extra material won't net you that much smaller of a chamber. Someone correct me if I'm wrong here, but I think they're around 74cc?
You might look for a set of '69 4bbl heads as they already have larger ports, larger valves, and a "quench" 58-60 cc combustion chamber.
Again though, you run in to the how much $$ spent to get them as good as a new aftermarket head.
Compression ratio also is affected by the piston deck height. How far below the deck of the block is the top of the piston. That's another volume to consider when calculating the compression ratio. I think Ford Motorsport catalogue has the formulas for determining your static compression ratio. KB pistons also has a good page explaining this:
There's also a great article on "quench" distance. Hence the importance of knowing your piston deck height:
It's about half way down in the article.
Hope I'm not rambling on too much here, but as you can tell, I kinda like head and engine talk. I'm pulling an honest 400 horses out of my '69 351W, and still am managing 10mpg, and maybe 12 with a tail wind and keeping my foot out of it. And, that's with a C6, at 3000rpm at 75mph.
I'd still like to know what I'd get with an AOD, but that's a lot of bucks to convert, and I don't think they're as strong.
<font color=green>**Question for "the board"..
Is it that tough to swap in a AOD (not electronic E40D)?
I suppose I can still buy a lot of gas for the conversion cost and trouble.
Plus, this C6 has got 270,000 on it and I'll bet I'd have gone through 3 AOD's in that time the way I drive.**<font color=black>
The most important thing though, is to have fun while you're doing the build-up. Because it's kind of a Tim Taylor thing!
Hope you aren't coming up with more questions than I answered, but at least you've got a little more information to go with.
Oops, one more thing, if you haven't picked up the performer yet, I'd seriously think about the performer "rpm".
The performer is basically a stock manifold that's aluminum with a little smoother runners.
The "rpm" is much more performance oriented, and would match your cam better.
WD-40 Reverend Grip-Shift
85 Bronco XLT, '69 351W, C6-Shift Kit, 9"-Detroit, Dana 44-Tru Trac, 2" Lift, 33X12.5s