The noise seems to come and go randomly it's definitely not related to the engine being warm or cold. I have pulled the plug wires individually and did not find the problem. I would say the noise soind like there are rocks in the engine.

I started prepping her for removal. She's coming out this weekend.

i will take a shot at this and its just a guess could you have scuffed a piston skirt ???it will sound like a poss bad rod brng but in reality will be a scuffed piston . pretty easy to tell witch 1 if you can see bottoms of pistons . the actual piston will be black as though it was painted . it happens usually from to much timing . very curious as to what you find

Last fall my chevy p.u. with a 350 vortec had a noise that would come and go. I was very certain it was a collapsed lifter. At times it would be fine for days in a row. It finally ended up being constant after running it daily. I was very certain it was in the valve train until I did a massive burnout in front of a friend of mine. That was the end of it. I had several rather large holes in the oil pan and the engine locked up. I never did tear it down to see what it was. I have grenaded engines before and I always knew when it was a rod or a main going. This one here was unlike any others.

Basically what I'm saying is your doing the right thing by pulling it.

and the winner is.....
 

Loose flywheel. Pulled the engine today and the flywheel was loose. There is a pin that helps locate the flywheel to the crankshaft that he fallen out.

Does that pin need to be there? If so how do I keep it from falling out?

thats the dowel pin that locates the flywheel and provides the shear loading. the bolts supply the clamp load. it is supposed to be a lite press fit in both the crank and the fw. it didn't fall out. the bolts loosened up because they were not in properly for one reason or another and that worked the dowel and killed it. if a new one is still a press fit in the crank then the fw can be fixed or replaced. a good machine shop can redowel the crank if its not.

Fixing it?
 

Is it possible to replace the dowel with the crank in the block, or do I have to disassemble and remove the crank?

Thats where I was going with my original post. If the dowel will not press in tightly (to the crank) then I would pull and send off to get machined. Do it right or you will fight it all over again (build a dozen or so 406's a year). Check your flywheel dowel hole real well to. If worn I would pitch it (I would) you can get it machined and bushed. Remember that the fly wheel "should be" balanced to the engine (if the builder did it right) so if you go new you will be looking at a balance job. Pete

the key will be whether the hole in the crank is ruined. if that hole is good, you can do a few different things all of which will work IF the hole in the crank is still good.

1) a good machime shop can bush the original flywheel to make a new dowel fit properly or

2) a good machine shop can make you a stepped dowel where the minor diameter is the original size to go in the crank and the major diameter is a press fit to a new oversize hole they make to clean up the original hole in the fw.

3) you can buy a new flywheel and have it balanced the same as the original

all the machine work required needs to be done by someone very good that understands what is required. the tolerances to make it survive are near zero. a dowel pin works because it has minus zero clearence. if anything at all is loose or wobbles at all then you are wasting your time. just having something to plug up the hole is not good enough.

Fixx
 

Later mobel GM's did away with the doll pin's.. so i guess they say its not needed anymore..

Anything that wasn't external balance from the factory (350, 396, 427, etc.) didn't come with a dowel pin. Only 400's, 454's, and later model one piece rear seal engines originally came with a dowel... for the simple reason of preventing the weighted flywheel from being installed without being oriented correctly. Thus, the dowel pin is not a necessity.

From a balancing perspective... the dowel is about 12 grams, placed an inch or so from center. It's not enough mass at a great enough radius to cause an issue.

Personally, I'd leave it out and not lose a bit of sleep over it.