I just wanted to know the main things that will cause a 440 to start running rough and missing under throttle? It can idle but its pretty rough and you can hear the slight missing, in some cases it will actually die. So what are the common causes of this and or problem areas? Thanks

Check for a carbon fouled spark plug and or bad plug wires. Very common for a miss under load. Even if the wires and plugs are relatively new it happens more than a person wants to think. Sure there are a lot of possibilities but that is where I would start.
If you have just done something requiring that the plug wires be removed make sure that 5 * 7 are not reversed on the plugs. Very easy to do and makes for a very light miss till under load being they are so close together.

Okay thanks I am definitely going to check my wires as i think one or two might be corroded. Around the time this started happening my ammeter readings have been kind of odd too, while idling the needle is just below the mid point so it looks like my batt is not being maintained. I figured the gauge was just going bad but could this have anything to do with my missing? THanks

Check our battery condition then. Low battery charge can cause miss fires as if you have electronic ignition it take a minimum of just over 12 to maintain constant ignition. Check you terminal condition and your grounds. Make sure terminals a shiney clean (both post and clamp) and tight. As for plug wires it is not always the terminals that are the culprit but they 'braided' conductor inside the insulation that deteriorates or gets stretched out of shape.

Is there a way to test the alternator and see if its going bad or if the problem is with another component?

There will be a hundred guesses, and all of them might be right.
Follow the instructions for a full tune-up. This should include a starting/charging check, compression check, full ignition check and replacing wear components, and a fuel system service. Then you will know exactly what you have and that the components are in good shape. Anything else is the shotgun approach.

I would start pulling plug wires one at a time to try and isolate which cylinder is the culprit. I hate to admit it... but I got talked in to trying the E3 plugs in my new build. The engine always had a slight miss that I couldn't figure out. Today I saw a reflection in the head on #7 and the spark was arcing up in the plug boot. Switched to an AC plug I had lying around from the old motor and viola! no more arcing or miss.

Needless to say new NGK plugs are going in tomorrow!

Okay good stuff thanks for all the input guys, what do you make of that ammeter reading I have been getting? Should i take it as a bad gauge or something more? THe battery is never drained and I always have power so should i look into it more or will the defect be elsewhere? Thanks

Double check the Firing order of the spark plug wires , you never know.

Spend a few dollars on one of those diagnostic testers at Harbor Freight. Test the resistance of the plug wires. An old timer told me this trick. I have found even NEW wires to have too high resistance to fire properly! Aim for no more than 1.5 ohms of resistance.
I have also heard of guys waiting until dark to check things. Have a buddy open the hood and watch the engine as you are inside doing a light power brake....not enough to spin the tires, just load the converter a little. If there is ANY sign of light coming from any part of the wires, you have found a problem.
I had an off idle miss in my Frankenduster awhile back. The coil was bad in my case, but it also had a vacuum leak. I had changed the secondary spring months before and didnt tighten the screws to the pod quite enough.

Well turns out that the alternator was shorting itself out and my volt regulator was fried. Both problems solved and the ammeter is now showing a charge again. But when I use my brakes and turn signal or brakes and headlights the engine starts running rough again and the ammeter dips well below 0. Didn't do this before so and thoughts on why it would start doing this? Thanks

Thoughts are that your engine is running on alternator current and the battery either needs a good charge and connection cleaning or replacing. When the brakes or signals are on you are drawing the alternated current down to a point where there is not enough to properly fire the engine because of low battery voltage.