I'm with you on splitting the cases...but just thinking about where the rocks could have traveled. I believe the only opening in to the center is at bottom near the shift drum or oil drain plug. It is currently obscured in your pic by black sludge. Clean that out and you'll see the opening. So, really any rocks that get through there should be sitting on the bottom of the cases? If you are not confident on splitting the cases one might thoroughly, very thoroughly, flush down through crank area, shake and tilt to drain through that little window at the bottom. Due that several times rotating the internals until you are confident that no debris remains. It would great if you got no evidence of rocks on the first flush but really, do it several times. Use diesel or kerosene as it will clean the sludge out from where you can't see. Of course splitting the cases would work too.

From where you are looking at the pics, you'll need to flick that Cclip off & the spread the legs of the two arms behind it that are operating the drum pins & slide that straight out & off. Then behind it is a plate held by two smallish screws-remove that. Then the crank nut on the gear you can see. i'm thinking pull the right side case off as i'm looking at it in the pic. I say that because it'll slide off the crank bearing on that side. Do remove the sprocket nut anyway as you'll need to to pull the gearbox out in the end. Oh, & pull the bung underneath on the left that houses the plunger & spring for the selector drum. But if you pull the right side then everything stays in the left. Once the crank nut is off, plus the other bits i mentioned then tap the crank end with something like wood between the hammer & the thread, or solid plastic or nylon. Hold onto the cylinder studs sticking up to support it then with a few taps of the crank & occasional tap of the gearbox shaft & the other shaft where the kick idler gear runs it should come apart--after undoing all the case screws of course. Look closely for all the screws in the dirt plus the one you can see in the pic looking through the hole for the magneto loom. I got a bsa gearbox apart once with one screw hidden behind things--wasn't good lol. Push the selector drum too but just by had to keep gears & shaft staying over in the left. If ya get that far ok, then come back as a crank puller/pusher is needed to get the crank out of the left side as is a tight fit on the bearing. Gearbox internals will now come out of the left case although might be a good fit in the output bearing & is two big Cshape retainer things with a thin washer keeping them together for assembly purposes. Study partzilla links might help. Some manuals can be confusing & i've seen haynes manuals jump to different model pics halfway through instructions so pics don't relate. That'll get ya started--if you've not fallen asleep with me boring you haha.
www.partzilla.com/catalog/yamaha/motorcy...973/rt3/transmission
www.partzilla.com/catalog/yamaha/motorcycle/1973/rt3/shifter-a

In my woffle above i think i forgot to say when the crank nut is off then pull the gear & the crank key that locates it before you start tapping things--pretty obvious though. Hope it goes to plan.

hello thanks again for the replies and advice wont get back to the bike till the weekend i might get a few hours on it hopefully then ,Heres a rundown of the bike so far it has a few problems firstly the stones in the engine was not on my problem list the reason i was stripping the engine was because the top of the piston had like shattered round the edge exhaust side,, and theres a small bit of it near the decomprsion hole about a half pea size welded to the barrel (ive got 0.5 oversize piston and hopefully gona get a rebore )wen, i took the exhaust of and put it down about a tennis ball size pile of rust just came out with bits of piston and rings in it spoke to my freind he said i need to strip the engine to get the bits out, but if there is a way to flush it out without splitting or would you recomend splitting , if i do have to split ,the instructions rt325 sent are sound ill bin the manual and follow those i attached a pic of the bike below as you can see it needs a lot more after the engine but need to no i can fix the engine before i start the rest thanks again

Well partner I’d probably retract my post of trying to simply flush out any small rock debris. With pieces of piston in the mix now I’d recommend splitting the cases.

...and the reason you need to do this is the debris you had from piston & rings is into the crankshaft rod big end bearing, as well as the crank bearings. Crank bearings are easy with the cases split, but you need to have the crank rod big end bearing re-done, as that's not something that takes well to debris showers, even after cleaning it out. The damage was already done, and you will have a big end bearing failure, if not right away (if just flushed out) but at some inopportune point during a ride. Speaking from experience. When the big end bearing goes it just takes out your fresh top end as well. Just good insurance based on your tear down.

hello thanks again for replies ive started to try and split the casses but didnt get far i removed the gear selector thing do i need to remove the drum with pins behind it and i cant seem to loosen the crank nut is there any tips on this im assuming the crank nut is the one im pointing to with the screwdriver on pic in the manual it says lock the crank with 2 peices of wood and a bar which is what i think i have done in pic but then watched some vids on youtube and they lock it with cluth basket jamming cogs also some say its opposite thread is it i dont want to put to much pressure on and snap conrod by turning wrong way any tips would be appreciated thanks

why its put pic on 4 times and split my text i dont no im obviously no good with computers either

That's probably where you left your cursor, in the middle of your write up. Then you probably inserted the photo several times thinking that it wasn't working, but it was inserting them where you left your cursor.

Not that I've ever done that........

Yes.

You can probably edit your post - delete all of the insertions in the text and then re-insert at the very end.