I have some scratches in my cylinder, I am rebuilding the engine and have taken the top end off. I don’t have tools to hone or rebore the cylinder. If I take it some where to get it fixed are they going to want the whole engine? Sorry if this is a dumb question.

No just take your cylinder, piston and rings  to your local Yamaha dealer and they should tell you if it needs honing or a bore job

How bad is it. Pic would be good please if pos. Are you doing a reto or just want it usable to go play on. A few scratches doesn't sound bad. But there's bad & BAD.

They aren’t the best pictures, one I can run my fingernail through.They aren’t the best pictures, one I can run my fingernail through.

Ok, i went back & looked at all your posts 7 i see the piston looking pretty marked up. But the rings are free & she'll run good. so shovel it back together & lets hear it run before wasting money. Not sure if you ever saw mine. I'll see if i can link my post from years ago without hogging your page.

One thing i noticed on my HT1. When the compression was down , it would take quite a few kicks with choke to get it to fire up. When i looked at the bore, it was marked up and had a couple of marks in as you described . That was because the rings had stuck back and the area the piston had contacted marked the bore . Get the free download for the workshop manual and check the piston clearance on the cylinder to the piston skirt . I bored mine to point 50 as point 25 might not have got mark out at the bottom.
After that, first or second kick from cold with choke and first kick when warm. Getting the parts for your bike is a doddle in the US. A piston alone here is getting on for 100$ by the time i get it in the UK.

Sorry to fill up your post with my rubbish. Found a couple of pics of mine as found. Locked solid with i guess piston corrosion to the bore but just forced it free on the flywheel with a long lever. Welded up a bend for the rotten header pipe. Found a tank as old one had rotted through. & pretty much went racing haha. Appologies to those that've seen it before. Video plays if you hit the youtube name on the video, well it works for me here. Gets a bit boring so drag it on. All i'm saying is i'm sure yours will go well as it is. Rings look free in the grooves. Mine sat on 55mph all day with my boy on it against school kid built bikes. Was years ago about 2017 or so.
I see he has a hell of a lot of videos up there if you want to go looking by hitting on his youtube subscriber name.