This spring when I started up my Dt125a/At4 up I looked it over and discovered that the
base gasket was protruding on the right rear corner. It started and ran fine, however, I 
didnt want to risk a seized top end. Back inside the skinning shack she went. 

Eventually I took the top end off and this is what I found in the photo above. Light scor-
ing on the intake side of the piston and bore. It didn’t clean up with light stoning like I
hoped. 

Heres the facts of the bike. 2800 miles on a 2nd over bore job 3 years ago. Last sum-
er I tested the compression at 130, same as when it was fresh. The motor and complete 
bike was taken down to every last bit and all bearings, seals, and other wear items were
replaced when it was rebuilt by me. It was the first time doing all of that, so I used 2man-
uals and the forum for guidance. It has run great for 3 seasons. 

I didn’t leak or vacuum test it before the top end came off because I only planned on 
changing the base gasket and it was still starting and running strong. Once I saw this, I
recalled that last summer the head nuts had backed out on me and kept it from starting. 
Learned to check those often. 

Is is my expectation that that was the cause correct? How do I know whether or not it’s
ok to put back together and run or if a rebore is in order? I can feel the grooves with 
my finger nail, but it does not catch. I appreciate the input and don’t want to ruin this top
end, but I don’t want to rebore unnecessarily as it 2nd over already. 
 

I'd give the cylinder a light hone to make it look prettier & don't worry about small lines. Then fit a new piston kit. But check the clearance as wonder if it seized back when it was bored oversize & possibly bored too tight or ridden a bit hard & overheated early on after the rebore. Only have about 1.6--1.8 thou clearance. Looking at the piston i guess it looks like 'that' on the exhaust side too?. Maybe richen the mixture a notch on the needle & go up a size in the main jet above standard to keep it cooler after fitting a new piston. You'll soon know if its too rich like that. I'm guessing its an electric start model, as we get both in nz. Is the timing close to right & the auto advance operating ok plus is it set at 1.8mm btdc. Bit of a bugger not knowing the cause. Bike looks nice & same tank color as an electric start one i had about 30 years ago.
Meant to say that even though the base gasket was damaged i guess your saying it wasn't sucked right in so not sucking air.

RT325, Thanks for your reply! I apologize that I didn’t reply sooner. Work picked up at my new railroad and I wasn’t able to get back to you.
Only the intake side was scared up. The exhaust was not.  We measured the bore, piston, and rings. Everything is still within specs. I was going to clean up the piston and run it for the summer. In the end I decided to get another second over piston and rings and carry on with a light hone as you suggested. I took it to the guy that did it the first time and he said that it would be all that was needed. Turns out to be an easy fix. Paid the same for piston and rings as I did for piston alone 10 years ago. Hopefully I’ll have her back together in a week! 
Is there any break in required in this situation? 

That sort of damage on only the intake side is lubrication related for sure.  Do you give the cylinder and piston a generous coating of two stroke oil on assembly?  Make sure the oil pump feed line is fully bled? 

Other than that I suppose it could have been caused by left over honing grit after the bore job.  They can be surprisingly dirty even when they look pretty clean.  A freshly bored jug should not be installed until a paper towel wet with solvent comes off of the cylinder wall clean.

Had to read back what i wrote last time--bad memory lol. Hope it goes well. Unusual 'i think' to not have seize marks on the exhaust side as well as it has to push out on both sides to seize i'd have thought. Anyway, look forward to the outcome.

TurboDan, RT325, thanks for the input. I’ll check pump output and make sure the parts are clean again before reassembly. I feel, although I cant prove, that it had to do with the head nuts backing out enough that I found it by the head clattering. It still started though! If it wasn’t that, then maybe from tuning it to run optimally in all conditions led to running it too lean a time or two. I dunno.  I’m going to put it back together and get a head temp gauge to monitor it. Then I’m going to add the head nuts to my pretrip. 
Ill update when I get things back. 

Also check that the air filter system is okay...  in my experience a little dirt getting through the filter tends to scuff up the intake side.  Or could it have sucked a bit of dirt through the base gasket?

Might be a good idea to run a little premix until you're sure the pump is good.  The "books" say that lack of lubrication causes that kind of scuffing but I can't say I've ever been that lucky.  Always scuffs and scores all the way around when I've had an oil failure

(never had a pump fail but I have had other issues like someone putting straight gas in a premix bike, not mixing in enough oil, or "mystery" causes like once a friend's bike had mystery gunk in the oil tank like someone poured water or antifreeze or something incompatible into the oil tank.)

I tend not to think it’s a lubrication issue as the pump went through the time machine in ‘17. Yep, that one. Also, when I took the top end off, everything was beautifully coated in yamalube. But I could see where it could’ve sucked something in off the top of the cylinder as there was some buildup of crud there. 
The intake system is new and uncompromised. 

Never had head nuts back off & just plain shouldn't happen unless the studs have pulled in the alloy but your model never really did that as those studs are in the crankcase good & solid. If the head gasket burnt out from inside out then yep they'll go loose. Tis unusual.

Is that a two ring piston as can only see one clearly. Just thought it might be an MX type single ring piston. Probably the dykes L shape top ring & i can't quite see it flush with the piston.