Bad Vibration at 2000-3000RPM

Balance is most likely for shaking like an expletive (like it will fly apart) at that RPM. The RPM is a specific clue, like a tire that vibrates at highway speed.
Shop mess ups happen, and when they do, it is much worse than a misfire, and is very memorable.

But before tearing it apart,
check the plugs to see if one is different. And check to see if you have spark at each plug. To do that, you can check the wires with an ohm meter and inspect the ignition components. But there are variations on this gadget to see if the spark system is working at each plug. I’d be more comfortable with electronics to try this rather than pulling one wire at a time. If the high output system is not phased by it, a leaky boot will light up your life and the headers are often darn hot.
Lisle Spark Tester Amazon product ASIN B0002STSC6View: https://www.amazon.com/dp/B0002STSC6/ref=cm_sw_r_cp_api_i_VMCHJZPRQJT5N1SBY1PP
 
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If your engine shakes whether its in neutral or drive it could be a multitude of things but my first thing Id say to check is the coil and how its wires for + & -....MSD is made in China....

Without doing a leakdown test its hard to say without whittling down the questions....

When your engine runs what does a vacuum gauge say??????

Have you tried disconnecting the mallory and tried running it without it?

What type of alloy pistons do you have and whats the bore to piston clearance?

Whoever did the machine work did they use a torque plate and did they align bore the main caps for the stroker crank?

Are you sure all the chamfer sides on the rods are facing the crank fillets?

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The other thing I saw others suggest is it being possibly the bellhousing alignment.....It is very important but if it does it in Neutral and driving its not likely.....

I got mine down to almost dead nuts perfect but anything more than .010" out is too much and must be adjusted using offset dowel pins......

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Good Luck figuring it out..
 
Yeah sorry I did I replied twice though. Yes at 2500 setting timing it vibrates the whole time. My timing at idle is 32 degrees. There is no change from idle to 2500 for some reason. I’ve tested it multiple times. I don’t understand the setup. I bought the car with that ignition setup. Firing order for f303 cam is 13726548
I can’t imagine a reason to run 32 deg timing. Try backing it off to 14 - 16 deg btdc to see if it makes a difference. Are you using vacuum advance in the distributor? If so, set the timing with the vacuum advance disconnected and the vacuum line plugged.
 
I can’t imagine a reason to run 32 deg timing. Try backing it off to 14 - 16 deg btdc to see if it makes a difference. Are you using vacuum advance in the distributor? If so, set the timing with the vacuum advance disconnected and the vacuum line plugged.
I think @Jarhead67 said the distributor is locked out. So whatever he sets it at will be the total timing. 14 deg will idle fine, but will be a dog under full throttle acceleration runs.
@Jarhead67 let me know if I have the right thread.
 
The crank, flywheel, balancer all went to machine shop for balance yes. And if it’s clutch then wouldn’t it not shake if you push the clutch in? Cuz it does
I know this is an older thread but in case someone is searching to solve a similar problem:

Disengaging the clutch removes the clutch DISC from the rotating mass (and everything else from the transmission rearward), but NOT the pressure plate. The pressure plate is a heavy component with the potential to cause a large imbalance.

If one forgets to install any required dowel pins between the crank and flywheel, or between the flywheel and pressure plate, enough misalignment between components might occur to cause some imbalance.

If none of this is the case, I'd suspect the possibility an error was made when balancing the rotating assembly.
 
I am pretty sure that there are no dowel pins between the crank and the flywheel on a small block Ford. Only ones I know of are flywheel to pressure plate, block to bell housing, and cam shaft to cam gear. There are also the rolled alignment rings for the head to block and timing chain cover to block but that is it.

I would have like to have known if the pressure plate and clutch was also balanced with the combo. My 331 was balanced and then the machinist put my RAM clutch steup on it just to make sure the clutch package did not have a problem. But I digress and being that this thread is over a year old and OP hasn't been seen since May of last year I doubt he will see any of this.