I agree...no way a 454 balancer and a 427 flywheel should work...something is WRONG with that deal as well...I bet you serious $$$ the balance WAY off and questionable if can get balance correct...I work with a great engine builder and we talk all the time...I had to redo a factory GM 454 last year that I bought brand new...had a vibration(not bad) about 1800...was in my gibson..ran it for 2 seasons 125hrs...spun a rod bearing..now this engine spent it's entire life @3200 never saw 4000...pulled apart had a scat crank in a new GM engine..bought another one they sell as a factory balance one for GM....my guy said he was barely able to get balance right..with balancing !! so if yours vibrates like that pull it out...take to a good engine shop now...as it will not stay together...at least you will know what you have there...now..all we know is that the pin has been removed !!
if you search on here about procomp heads you get a earfull on what other have found...so I can only imagine what the cranks/rods are like...

Not trying to bum you ,but because of the problems you are having ,,,have you attempted to just get your money back..
In the link that was provided that motor sold for 2600 and change ...Is that what you paid ?Good set of heads cost more than that .....
TRY to get your money back .....JMO
FWIW I had seen those motors before at something more than 2600 and was curious as to the quality of machine work .I already know the lack of quality of parts...Sorry chief

This would be the first and easiest thing to check.

Im planning on pulling the engine in a couple of weeks to see what flex plate is on it. a few people are telling me to run a fluid balancer on it. and if so what flex plate do you use. external or zero balanced?

No fluid balancers in a boat. After the boat sits (in some cases months at a time) the fluid settles in the bottom of the balancer and when started it will snap the crank nose off.

First of all, do you have data or facts to back your statement that if using a Fluidbalancer, the fluid settles in the bottom and at start up snaps the crank off? I have been doing this for 23 yrs have used Fluidbalancers from Fluidamper, and have NEVER, had an engine vibrate or break a crank after sitting or cause bearing damage due to harmonics from the balancer.
Now on the build; if typically building a 4.250 stroke engine, the engine should be balanced internally, needless to say; I have seen engine over 4" stoke balanced externally. If the rotating assy was balanced either internally or externally, the balancer and flywheel should be verified either to be neutral or counter-balanced. I have seen externally weighted flywheels drilled on that will change your balance, if the same flywheel or balancer is not used during balancing, same goes for a neutral engine. Some times people are Lazy, and they drill the flywheel, when it should be neutral. Have someone verify the flywheel is neutral.
They could have made a mistake adding or measuring the bob-weight, totals. This is usually noted by experienced professionals, knowing the average weights used with the pistons and rod combinations used in the past. BBC around 2300-2400 grams total, then divide that in half for each half of your bob-weight.
Hope this helps, Mark

No personal experience but that's what I was told by the folks I bought a crank from (no names, not throwing them under the bus). Also read about it on line. Could be nothing but why take the chance? It's kind of believable. Maybe you buy better ones and it's just the cheaper ones. I don't know.
But I cant see why you would want one if you are balancing a motor anyway.

they do not use flex plates, std trans flywheels, the external or not flywheel/balancer determined by the crank...most std 454 use a external counter weight....but they are a few differences gen IV vs VI as well as some aftermarket cranks...most stroker cranks use a zero weighted one...

well I brought the boat home from havasu to pull the motor and I did that today. it has an external balanced flywheel and balancer on it just like the engine builder said to use. do I throw all neutral balanced on it and see what it does or do I tear it down and have it balanced again.

"THE CAMSHAFT IS A NEW ELGIN INDUSTRIES E1143P AND WITH A TRUE CLOYES DOUBLE ROLLER CHAIN SET. THIS CAMSHAFT IS A HYDRAULIC LIFTER GRIND .576 LIFT 246 DURATION @.050 ON BOTH THE INTAKE AND EXHAUST AND IT IS GROUND ON 108 DEGREE LOBE SEPERATION. THIS CAMSHAFT HAS A DISTINCT LOPY IDLE AND IS DESIGNED TO MAKE MAXIMUM POWER IN THE 2500-6500 RPM RANGE"

I'm no marine eng expert, but if you're going to tear this eng down, might wanna consider replacing the cam. This one doesn't sound boat friendly.
Maybe one of the more experienced guys can weigh-in on this.