Hey, sounds like a fun project--I have a '72 F100 with a 390/C6--great trucks.
First you need to baseline the main components.
First and most importantly, you need to figure out your compression ratio. Did you take any measurements when you had the heads off? 360 FEs came with very low CR from the factory--if yours is low, you are going to fight getting power out of it until you get the CR up to 9:1 or higher. I hate to say this since it requires you pulling the engine and investing in pistons, but you'll just never get that engine to live up to potential with a 8:1 CR.
The fact that it ran great and then fell off right after break-in combined with an used cam makes me think that you might have wiped out some lobes on the cam. Buy a dial gage and magnetic mount from harbor freight (or borrow one) and learn to use it by measuring the lift at each valve. If that engine doesn't run smooth, that would be my first check.
No matter what here are some simple things to do.
1) Map the advance curve--you can do this with a dial back timing light and a tach. The trucks normally had very slow advance curves and this hurts power. A recurve spring kit from Mr Gasket is a couple of bucks and can make a big difference, but don't do it without measuring the advance after you put the lighter springs in--you can get into bad detonation if it's too quick. Of course if your CR is the low factory rating, then it would be hard to be too quick for that motor. Initial should be 14-18 degrees and total should be around 36 degrees (vacuum advance disconnected).
2) Carb tune. Once you dial in your ignition system. You need to read the plugs and see if you're carb is dialed in. A little rich is OK, lean is bad. You'll want to confirm that your secondaries are working right.
3) check simple stuff like your fuel filter--if it's partially plugged you can be starving the engine at higher RPM.
hope this helps and welcome to the forum
http://www.supermotors.net/vehicles/registry/9026
