Does it still do the same thing when you remove the chain?
If it doesn't, try this to see if it's the transmission/engine:
-Remove spark plug
-Remove chain
-Rotate engine over in neutral by hand with kickstarter and listen for sound, if not present continue to next step

-1)Put into gear and rotate engine, check all gears, listen for sound
-2)Put into neutral, remove chain from rear sprocket to bypass axle, pull the engine over by hand with chain, listen for sound.

If you can isolate it to the engine, then you know for a fact there's something wrong with the engine/transmission.
Before you take it out and apart, check the most accessible parts of the engine first.
Remove stator cover and flywheel, make sure nothing is loose, don't forget counterbalancer.
Remove clutch cover and look for any issues.
Drain transmission oil and check for metal flakes, shards, or lots of powdered metal entrained in the oil.
The idea is to inspect and identify the problem before having to spend a lot of time removing the engine and splitting the cases...that's the last step to take.

It only does the jumping when its in gear.I can spin the axle in neutral  no jumping.Only when i have it in gear.Im going to mess with it some more today if i fell better,Im a little under the weather.

Yup, sounds like a missing gear tooth.
Does it only jump in one gear?
Not that it's a solid indication, but it's a good way to troubleshoot.
A broken gear tooth can easily float around and break other gear teeth too.

Go to the store and buy a funnel with a screen at the bottom (or make something that can filter metal particles out of the oil) and drain it.
If you have a magnetic drain plug you'll probably find parts of it right away.
Run a magnet all over the bottom of the case to pull the broken bits toward the drain.
Go from the outside and slide a STRONG magnet straight toward the drain.
Alternatively, if you can fit a tiny magnet into the drain with a flexible shaft, you might be able to pick it up.
The point is to determine for sure it's a gear tooth, and a particles or teeth are a smoking gun.
Either way, it sounds like you're going to be splitting cases or sending it off for a rebuild.

It does it 1 threw 6 when jacked up.Does it worst without throttle.Im going to rebuild the motor just for peice of mind.I dont know how old the bearings are,It has had metal in the case when I bought it .But when i rebuilt if a year and half ago.I cleaned all the bearings up really good.Checked the transmisson when i put the new crank in it.Thats been probally 600 or 700 hours ago.I dont know how long before that.at least 2 topend now on the third one.I didnt fell well enough to mess with it today.But im going to mess with it tomorrow.Im going to go threw all possible issues first.Il keep you guys up to date on this issue.Thanks for the help.il let you guys know something tomorrow.I could have bought a new quad for all the money i have spent in this one.Its starting to really make me mad!

I much rather rebuild mine.It isnt to hard to do.I got good cases no broken bolts.I have had it apart once and put it back together and it was my first time i worked on 4 wheeler engine.I have learned alot since then.

If you were planning on tearing it down and inspecting/replacing transmission components anyway, why did you bother starting a thread?
Seems like the tear down would answer your questions right then and there instead of us trying to speculate about what it could be.
If there was metal in there when you took it apart and did nothing more than cleaned some bearings, then you put another 600 hours on it...the question should not be "what's wrong with it" but rather "is there going to be anything in there worth using again".
Furthermore, 600-700hrs is a LOT of riding...top ends rarely last more than 100hrs.
Have you gone through 6-7 overhauls?

It was stock.Just bored.Pipe and add ons.No port work done or anything like that..After 19 years old it was on it second bore,when i bought the quad.That was a guess on hours.I rode 6 to 20 hours a week.More then some .I do ride alot.100 hours seem really short life to me.I say all ported up thats probally right.But with stock ports its just getting warmed up. When i first got it.Also the only reason it went down the first 2 times.Was because the person i bought it from didnt put any thrust washer in the upper pin.After the second topend.I called Wiseco and they said i didnt need thrust washer with thier piston i was using.which the person i had bore it didnt know..Well they were really wrong..Well right at a year it beat the piston  up pretty bad It knocked the pins out of the piston were the ring seat over to keep them into place.  .Now i got rm bearing and billet thrust washers..Well in that rebuild i took the cases apart and put new crank bearings in and a crank.Well the oil plug was stripped.And when i put a helicoil in i got the shavings from the case in the motor.I spent alot of days cleaning it in a part washer.Which did work well because a year of riding with no issues.I do thankyou for your help.;I did find the problem last night.I done what you said with the chain off.The motor is tight.For some reason the bearing are rough in the carrier.So im glad i did listen to you and not get into my own way and take it apart to see nothing was wrong with it.The motor went threw all the gear didnt have a sound or a problem or a jump or a thump at all.Smooth as could be.So im going to work on the carrier here in alittle bit to fix the problem i think it is the spacer is too long and blinding them up.But thanks for your help and anyone who posted with idea to help.Il be back later to post my results.

ok so you say you need new axle bearings, if you do this they will last forever.
do you ride in creeks and big mud holes, if so before you put new bearings in.
the new bearings you get are a sealed bearing, take a 1/8 drill bit put 3 small holes
in the seal on the bearing on both sides and try to make them off set from each other.
just go through the seal,
then drill a hole in bearing carrier between the  adjuster bolts, put a grease fitting in there.
try to pack carrier with grease before you put back together. now you can grease your bearings
anytime you run through water, this will help keep them lubed and they will last a very long time.
you should be able to push your quad very easy, if you have to put effort in it then your bearing are bad
this is a easy way to tell, once you change bearings you will know what i am talking about. one finger can push
my quads across the floor,

John, Is that pushing your bike up or down the little slope in your basement?

The sick thing is GrkGuy.I just put new bearing in it.I have  Lonestar Swingarm with Lsr carrier.It has the grease fitting in it.But the sick thing was when i had my durablue axle in it.It was like the spacer was too big and was making the brake side bearing stick.Well the axle keep spinning and it tore the material off the axle cause the axle not to seat on the bearing no more.So i bought a Lonestar axle new.I didnt want the spacer to lock the new bearings up on the new axle so i took my grinder and grinded the spacer down some, for  more room.Well it was too small and binded bearings up and made them drag, where it pushed them together.Well i tried using a spacer out of my stock carrier and it was too long and ive been trying to grind it just right.Well i got it too short and destory the new bearings.Well i look on lonestar site and they got new carrier kits that come with bearing and seal and spacer for their carrier for 84.00$.So im going to have to go that way now.Il tell you one thing if it was raining women outside I would get hit with nothing but dvds of Magic Mike.My luck sucks!!!!

well then did you ever think since you already tore it apart once then that might be the problem. lmao

I had it apart to put a new crank and crank bearings.I check all the bearings in the transmission and transmission part year and half ago with no issues.

Is the frame solid? Check under the foot pegs for cracks.

what is your chain slack ? is adjusted  with correct sag ? when jacked your chain should have near no slack.  i always set 1" 1/8-1/4 max with quad resting on ground with correct sag adjusted. 

Chain is going to be the same tension jack off the ground as sitting wheels on the ground . When weight is on quad is when you want no slack. I fixed a while back  carrier bearings was the issue, well the spacer was the problem. Putting to much pressure on the bearings making them drag causing the chain to jump.