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Sudden Onset Chatter Issues - riding the struggle bus and need some HELP, please.

I know you did a nice rebuild of your lathe and I assume all of the slides were scraped and fitted good. I have had the compound slide to be the culprit of causing chatter. Most of the time it is caused by the gib being loose or snug. Unless you are using the compound for feeding, tighten the gib screws, not really tight but tight. This should calm down any chatter. The surfaces between the compound base and the top of the cross slide are another problem area. If not perfectly flat, it can cause chatter.
If it were a spindle issue, unless the bearing clearance test you did was somehow faulty, I would have expected a significant reduction by supporting the piece with the tailstock (although a proper test should have been performed with at most half of the bar sticking out from the chuck and with a dead center, not a much less rigid live center).
I suspect more and more that your saddle is high in the middle and is rocking, or that the bed has a serious twist.

The only thing I see not mentioned is the drive system. Check all belts and the rest of the drive for slippage. Good luck
I am still trying to chase this down. While I had the spindle out, I checked everything as best I could. The front bearing surface has some galling on it, but no more than what was there when I had it all apart 3 years ago. As best as I can measure it, the spindle is straight. When I had it apart the first time, I replaced the thrust bearing and also replaced the rear felt washer with a thrust needle bearing. I replaced them again today.

I ended up replacing the front bearing cap shims with a set from eBay. Installed, the front bearing was within the .0007 to .0010 spec without removing any layers. The rear ones were too thin. Slightly snugging the rear bearing cap screws and the spindle binds up. So I put the original ones back in. I did end up removing one layer off of one shim to get it within spec. Both the front are rear bearing clearances are within spec. I ran the lathe for a while tonight, but I will check them again over the weekend.

I also tightened the V belts between the motor and the countershaft. They were a little bit loose. Not overly loose, but likely stretched a bit.

I did some test cuts. It's better. Not as good as it was, but it is better. Depending on material, that is. 12L14 machines pretty much perfect. Where the 1045 that I had no issues with a couple of months ago is now giving me fits. I machined a new splined shaft from a stick of 1045 and didn't have any of these issues.

I didn't notice any rocking in the saddle, but I am going to recheck it this weekend. I'll also recheck a bunch of stuff I already did. I need to document all of the steps and results or I'll lose track of what I did. :)

So my next this to try is to drop the motor and check/replace the bearings. I don't want to drop the countershaft unless I have to. That would likely be the last resort in trying to chase this down.

It could have been a combination of a bunch of things all coming to a head and correcting some of the little things is giving me some improvement? We shall see.
Here's fairly wild swing at your problem but it is a possibility....although remote. While the lathe is running, put your hands on the motor itself and see if it seems smooth in operation or if it has a "buzzy" feel to it. The fact that you say that this issue popped up almost overnight makes me wonder if something has gone wrong with the drive motor. The motor shaft bearings could certainly cause a problem like this if they're bad enough.

But I think back to the issue we had at a small shop where I worked part time for a while. They got in a new "Pacific Basin" lathe with a 2 HP single phase motor on it. The lathe would not turn a part without leaving an odd pattern on the workpiece. It simply would not make a smooth finish. The drive motor buzzed like nothing I'd ever seen and it apparently was leaving remnants of the buzz behind on the finish the lathe would make.

We converted the lathe over to a 3 phase motor with VFD. Behold!! The vibration and strange pattern went away!

It is possible (remote as I said) that something has gone wrong with the windings in your drive motor--a winding coil or coils have started to fail with multiple turns shorting which would unbalance the motor magnetically, resulting in a buzz. In the case of the lathe at the shop, the motor was just built wrong. In your case, it could be failing although to be honest, once winding coils begin to fail, the complete failure and burn out wouldn't take much longer.

As I said.....just a wild swing since you haven't found anything else wrong.
Well, I can't say for sure if it was ONE thing, but I have my suspicions on what it was.

What did I do:
  • One of the rear leveling feet had come partially off the rubber pad, so I fixed that. I doubt that was it.
  • I adjusted the V belts on the motor a little tighter. Specification says I should be able to press them together about 1".
  • I did check the bed for twist and didn't find that there was much twist at all. One end was maybe out of "level" by .0008" over 10" - as precise as my cheap chinesium level can measure - .0002" over 10". The bubble was off by 4 tick marks. On a 5 foot bed, trying to get that out of it using leveling feet is a fool's errand. I tried, but made 0 progress.
  • I pulled the spindle and inspected everything. I set the spindle in the head stock bearing caps, put in indicator on it in multiple places, and saw no evidence of it not being straight.
  • I cleaned and stoned the front spindle bearing surfaces, on the spindle itself and inside the bearing caps. There is galling on it, but it's been there since before I've owned it, and it was never an issue before. Stoning it probably didn't do much at all. But if there were any burs, they are gone now.
  • The rear spindle bearing surfaces were perfect.
  • I stoned the mating surfaces of the bearing caps.
  • I flushed the front bearing oil sump and replaced it was new spindle oil. It was dirty - not surprising since it's the business end. The rear was perfect.
  • I bought a new set of layered bearing shims from a seller eBay.
    • The rear shims were too thin out of the box so they were useless. I ended up using the originals, but I did remove one layer off one shim to get the spindle play within spec. (.0007" to .0015")
    • The front shims were also too thin, but I was able to use them by adding a .0015" shim to one side of the bearing cap. That put the spindle play within spec.
  • I replaced the thrust bearing that's between the cone pulley and the rear spindle bearing.
  • I replaced the rear needle thrust bearing that is between the rear bearing cap and the take up nut. From the factory, this is a felt washer, but I think the needle thrust bearing is a better replacement.
  • I adjusted the take up nut so there is .001" fore and aft play in the spindle.
  • Along with the menagerie of other things I already checked and mentioned before.
The verdict:

This is some DC 53. If it was going to chatter, it would have. My lathe doesn't like this stuff much. :) I also tried a piece of the same stuff I used in previous posts. It's back to normal. Yay!

What do I think it was? I think it was the take up nut (mostly) and the front bearing clearances combined. When I removed the spindle, I felt like I remember the take up nut being a little loose. Not like flopping around loose, but just didn't seem like it was tight. Although I could be misremembering or merely hoping I have something at which to point. One of the tests I did was to tighten the take up nut, not knowing at the time that it needs to have some play, and that probably made it worse. I think it backed off a little as some point. And I think that plus there being TOO much play in the front spindle bearing cap, was what it was.

Lessoned learned: Do at least a yearly checkup on all bearing clearances, belt tension, etc.

Thank you again to all who offered suggestions. I read them all, even though I did not reply to all of them. You gave me hope!

That's fixed! On to the next job!
looks like you solved the problem, good.
When having chatter i like to swing my compound a few degrees to the right, enough so any build up of cutting forces swings out reach away from the part.
Think about the tool holder swing/rotation being on a big radius and setting the cutting end length being a little to the right of center on that radius.
You may get a box of inserts that not at the peak of sharpness, that can magnify this problem.