Swarf INSIDE the gear head

I've been going thru a 1958 LeBlond Regal 13x40 manual shift. I did the apron and QC box, everything was fine. Over the w/e I'm draining the head oil to put in some fresh DTE 26 and I see what appears to be a roller from one of the bearings sitting on the bottom, WTF? I took off the cover when I bought it and looked at the gears and bearings it felt great when turned by hand. As it turns out the "roller" was actually a straight pin that locates the main gear cluster axially on the spindle. It goes into a hole on the gear hub and into a hole that is bored into the spindle. The hole in the spindle goes all the way thru to the center bore. The gears are also keyed to the spindle. When it came out it allowed any chips inside the spindle a direct shot into the case when they hit the hole. I took about a tablespoon of the stuff out. Amazingly the bearings all feel great with the exception on the input shaft, it feels a little rough probably because those bearings are the lowest in the case and may have got a chip or two. I've got the drive pulley off the shaft and the bearing retaining flange removed. I'm going to try a slide hammer to pull the shaft/bearings, if that doesn't work then rig up a puller with a piece of pipe and threaded rod. I guess the chips must have just sat on the bottom of the case, pretty amazing. Anyone got any suggestions on removing and replacing the shaft/bearings? Thanks.
Steve

It's possible for any amount of debris to find its way into a geared transmission. So long as the stuff is heavier than oil and sinks to the bottom and never gets churned up by the gears ro sucked into the oil pump it could stay there for generations.

Its much better if there's nothing but clean oil in the sump and maybe a sump magnet. Clean it out good and troll a magnet around the corners and obstructions. If you find anything you cant get at and you don't want to dismantle the transmission, sometimes it possible to clean it up as best ou can, flush it wirh mineral spirits paint thinner, then wall in the adherant debris with a suitable paint.

The next step is to fix that pin in place so it stays put.

I blocked up the head end of the lathe, the drain plug is on the bottom of the case right behind the chuck. Then I took one of those pressure tank sprayers that are used for spraying weed killers. Put about a gallon of kero in it and pumped it up and adjusted the tip for a heavy stream then flushed the case with it. It works great. Let it drain thru a funnel with a screen in it to take the big chunks out. Then strained the kero thru multiple layers of paper towel to take the fines out and flush again. I must have done this 20 times. It is clean. This is a great way to flush something. There is enough pressure to move any chips and blow any particles out of the bearings.

When I cleaned the headstock on my Clausing, I flushed it out and didn't see much crud. I added a pump and used one of those glass carburator filters that you can take apart to clean the screen. After a period of time I had to clean the filter due to tiny particles plugging up the filter. It has been ok since then.