I have a 383 that I ran in my camaro for a year.  When first built the rotating assembly was balanced at a machine shop and I assembled the engine.  It was balanced with a 400 balancer and flexplate.  This weekend I pulled the engine out and installed it in my 77 chevy pickup with a four speed.  I bought a 400 flywheel from autozone thinking thats all I needed to do.  As soon as the engine started, I noticed the vibration!  Did I get a bad flywheel, or is this imbalance not going away whithout pulling the engine apart and getting it rebalanced with the flywheel.  Has anyone ever switched from an automatic to a standard with a similar engine combination? 

I had the opposite, I removed a manual trans flywheel and replaced it with an automatic flexplate.  You don't need to tear apart the whole motor for it, all you need to do is have the new flywheel balanced.  you should be able to take the new flywheel and have it balanced to match the old one. 

If I read you correctly, the original 400 was balanced at a shop with the damper and flexplate. Now you're converting the engine to a manual transmission by using a 400 flywheel purchased from Autozone. That may also mean that this part is made in China, and God only knows how close, if at all, it comes to factory specs.

The likelyhood of this new combination being in balance is pretty small.  Engine balance is a pretty tricky art form. The factory has their way and various shops have their's. The issue is buried some where between a number of factors, one of which is the philosophy of advancing the balance point, setting it straight up, or redarding the balance point. (The reciprocating components change their apparent weight on the crankshaft by the continously varying length of lever arm created by the stroke as the crank rotates. That's to say the weight seen at the crankthrough is not the same at TDC or BDC compared to when the throw is a some angle other than straight up or down. There is also the issues of varying cycle forces and gravitational effects.) The factory is balance done straight up. Competition houses will push the balance point around depending upon their approach to a "competition" engine. There are other considerations of this type that a shop will apply in terms of where maximimum balance occurs in the rotation cycle and where local unbalanced forces are allowed to exist. The 400 has plenty of these. While the entire rotating and reciprocating assemble may be in net balance as an assembly, there are many places along the length of the crankshaft that are not in balance with themselves or adjacent places. This reuslts in considerable local loading that causes twisting of the crank and harsh local out of balance loads being transmitted through the bearing shell into the webs and crankcase.

The long and short of it is that the engine needs to be dissassembled and all crank components returned to the balance shop to be redone, as no factory balance job will match that which has been done on this engine, and the flywheel can't be balanced to the engine by itself. That's not unusual, any engine balanced outside the factory will require a rebalance when changes are made to the rotating/reciprocating masses, assuming your flywheel is even within factory balance parameters.

Bogie 

I had my flexplate balanced to match the old manual trans flywheel, I didn't tear apart my motor to do it.  My 400 sees  around 6500 quite frequently and i've never had a problem with it.  

If frogs had wings they wouldn't bump their behinds when they jump. The ifs here being that CQUT, may or may not have balanced his flywheel to the old flexplate, sounds like not, but rather depended upon it being within factory specification. If the flywheel is made in America, it might be inside factory balance parameters, if it's a Chinese made item, which it probably is being form Autozone, then you can't just assume anything. I won't build anything with Chinese parts, but it's getting harder and harder to avoid this junk at any price.

If the engine still had factory balance he might have a fighting chance, but it sounds like the engine was custom balanced. That opens up whole new world of possibilities most of which means that a flywheel added at a later date, even within factoy parameters probably won't work anymore without being balanced to and with the rest of the assembly.

 He might get away with having the flywheel balanced to the specs of the previous flexplate and torque-converter assembly or he may not. If he has enough money to shoot craps and it comes up snake eyes, fine; if he doesn't have the finances to do that, then I really need to recommend that it all goes back to the balance emporium, a few hundered dollars investment might be better than a becoming the owner of a few thousand dollars of scrap.

As for your turning a 6500 RPM on what you did, I can't comment, it worked for you, that's good. An engine coming out of my shop wouldn't get that treatment, my customers do it my may or they can go somewhere else. My way is the long and expensive way round, cause I don't trust half measures, even though they can be successful from time to time. In fact I convert all 400s and 400 derivatives like 383s and 406s to internal balance, which is pretty pricey because the work to put expensive Mallory metal (Tungsten) into the counterweights is labor intensive. But these engines will run 6500 of better all day long. But I'm not even suggesting this to him. Just a little insurance policy.

Bogie