I am thinking this is in the distributor because I installed new weight springs,adjustable vacuum advance and pertronix. Any help would be appreciated.

You are checking the timing with the vacuum advance unplugged and the vacuum line plugged, right?

A normal timing figure should be between 6-12 degrees BTDC at idle. When you get a vacuum guage (Sears has them) adjust the timing and idle mixture for the highest vacuum.
And if you see the vacuum guage fluctuating, that indicates some problems, usually valve related.

a. Vaccuum line disconnected (else you'll be letting vaccuum advance upset your timing).
b. Rpm low, perhaps 650 or less (else mechanical advance will start coming in).
c. Timing marks accurate (can be off for a number of reasons. Among them: degree ring has slipped; wrong harmonic balancer).
d. Incorrect plug lead selected (Ford uses passenger side for #1 plug lead).

vacuum advance doesnt matter because at 1000 RPM the engine shouldnt need 40 degrees timing to run smooth.

The second assumption and its a big one is that the marks on your damper are correct. I would choose to blame the damper marks at this point. You have to make sure that when cylinder #1 is at top dead center the -0-mark on the damper lines up with the pointer. TDC can be found by inserting stuff into the spark plug hole (some people use old pushrods or pencils). Make sure you get TDC on the compression stroke for #1 cylinder.

The cam timing affects breathing and compression, which might in turn make the engine run poorly, but wont throw the reading you get from the strobe out.

You should get a slight vacuum on the carb at idle (its basically the vacuum generated by the air filter and by the slight flow of air through the carb) That slight vacuum isnt usually enough to make the distributer move the timing, but you should disconnect it anyway. some engines have dual diaphram vacuum units which retard timing based on manifold vacuum, disconnect all hoses from the distributer AND PLUG THEM (without the plugs on the vacuum lines the engine can run rough due to lean conditions)

Think about what the timing light is. It tells you when the spark goes off relative to the piston position (assuming the damper is correctly marked).

I went and pulled the plugs out and found the #8 cylinder a little sooty so I changed the plugs and also did a compression check. The highest cylinder was 200 and the lowest 180 so for a new engine that is barely broke in, I think I am ok.

I restarted the engine and the only problem is when I turning the idle down and get close to 1000 RPM then it starts to pop. Not a backfire but a noticeable pop. I am starting to wonder if there is some kind of carb problem. I have a 4300 Autolite that has been restored by pony carbs a few years ago and have had no problems since reinstalling after the rebuild. Any more ideas?

The vacuum adavance you see would be a result of the amount that you have the primaries open in order to keep the carb working 'above the idle circuits' (for lack of better term).

Can't explain the 40 deg timing but seems that the idle circuits aren't working on carb therefore you are keeping it running with the primaries open - therefore you have a vacuum signal to the vacuum advance. My guess is that surging and popping would be due to fuel starvation when transfering to the idle circuits.