rotary cutter really knocking

I was mowing a couple weeks ago with a JD 727 14 foot mower. Ended up snapping the pto sub off the 4010 and running over the pto shaft. FInally got it all back together had to get a new tractor yoke and replace the cross bearing which gave me fits. ANyway, started mowing and the dog gone thing is a knocking something fierce. It almost sounds like the blades are hitting each other under the deck. There are two gear boxes and they each spin a bar with blade off each end. The ends of the blades are buggered up but that could be from hitting rocks. Its fairly constant and loud. ANy ideas on diagnosis and fix much appreciated.

PS- the previous advice on getting out the snapped off bolts holding the sub on was spot on. Left twist drill spun them right out.

How are the other u-joints? I assume there are more than one. It's unlikely anything could cause the blades to hit each other unless they overlap and need to be timed.
Is the shaft you ran over bent? Maybe it is hitting the shield. Or causing the shield to vibrate making a knocking sound. Turn the mower by hand and see if blades are hitting each other. Process of elimination.
Running over the PTO shaft leads me to think the mower came to an abrupt stop, partially shearing a key somewhere and throwing it out of time. Let us know what you find for our own knowledge.
Also look at the mount the gear box is mounted to to see if it got bent when the shaft hit the ground
I ran over something and had a knocking like you describe. The stump jumper was bent and causing the bolt that holds the blades on to knock the underside of the platform.

Hook onto it with the front loader and tip it up verticle. Then search everywhere for anything shiny.
I found if the blade is hitting anywhere on the mower frame it doesn't take much to make a terrible noise. I thought I bent my flail mower drum. I ran over a large rock, then a noise. I found one of the blades was bent just enough causing it to hit the frame. Stan
You saying you welded up a new PTO shaft??? If yes did you time the U-Joints as they should be or did you just weld up a shaft and not pay any mind to how the U-joints line with with each other>??? If you just welded up the shaft any which way yep it will knock big time and sooner or later things will start breaking big time
I didn't weld up a new shaft, just had to get a new tractor yoke and change the cross bearing. I'm thinking you guys are right, I bent something. The mower is huge and heavy, I need to winch it up on the boom pole and then prop it with some 4X6's or something and see whats going on underneath. The rest of the u joints seem ok and the PTO shaft isn't wobbling much, I think its blades hitting eachother or more likely the mower deck. That deck is made of some thick metal, they don't make em like they used to.
mattcatlin The JD 727 has an issue with the drive line. The slip clutch is on the input side of the gear case. So the two shafts that go to the outer gear boxes can't slip. So if one stops the other tries to drive it by Flywheel effect. I had one and if you hit some thing with one side it would tear up the drive line before the slip clutch would do anything. I know you had a failure on the front shaft but check the drive shafts and gearbox shafts going out to the two outside gearbox's. They can twist. Then they are out of time and the blades will hit the tips against each other.

That driveling issue is why I sold it and got a cutter that has slip clutch on each side and does not depend on timing for clearance.

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