No good reputation machine shop will touch a cylinder without a piston. That doesn’t mean they know the correct tolerances. Or’ if the customer is a total newbie.
asco

Might be a good idea for the OP to strip the top end, and I would guess the cause of the noise should be very clear?

@ASCO I wouldn't classify myself a TOTAL newbie, but I'm pretty close lol. I'm certainly not afraid to admit my ignorance or ask questions!

@TZSV4K As for them having the piston - keep in mind it happened a while back now and I was pre-occupied with starting school, so my memory isn't the best from then - I gave them the old piston and I do believe they had the new over-sized one before they did any work; however, I don't know what their procedures are! Quite a few people had recommended this shop to me, so maybe I was the one unfortunate soul who had the new apprentice machine my cylinder ahahaha. Once the bike fully warms up, the slap decreases quite a bit though!

I believe some of my worries/ concerns stem from just not being around old 2-strokes enough and having a solid feeling of how they should sound and perform. Additionally, I love these bikes and it would be awfully painful to have one blow up on me so there is a bit of a fear factor there too hahaha!

Why not strip the top end, and find out what is making the noise? Its a very simple job.

@YAMFAN Yes! I plan on doing that this coming weekend! I've just been dogged after work this past week so I haven't gotten to it yet.

When you have the top end off, check the bore clearance with feeler gauges.

Measure clearance bottom centre of rear of piston, and cylinder bore.

Take measurements with piston at the bottom of stroke, mid stroke, and top of stroke.

Can you post a video of it running so we can hear how much rattle before you take it apart 

Put a few extra ounces if 2 stroke oil in the fuel tank rock the bike with the front brake on and ride the bike for 20 minutes waiting to hear or feel a power loss. You can rebuild her.

If you’re not blowing up your projects you’re either afraid or not going fast enough. Trust your gut. You’re not experienced enough to determine what MIGHT BE WRONG. 

you’re getting bad information. 2 stroke engines are tough!

asco

In post #1 you said you had the crank bearings replaced did the same shop rebuild your crank we really need that video we all are guessing we are going down a rabbit hole 

Not totaly relevant but is the clearance on the piston--therefore being 1.5 thou .035mm under the stated bore size, or is the clearance on the bore--like first over 0.25mm + .035mm clearance.
I guess it doesn't matter if the piston is supplied to the machine shop with the cylinder.
Na it'll be on the piston? i think because Std sizes went in 96 97 etc so just under the std size.
Then again i'm talking myelf into a corner & could be totaly wrong.
Also piston rattle can happen even after boring if it didn't cleanup around the ports by a significant amount but doubt that happened or the shop would have said--need the next oversize or it leaves them looking bad if it catches up with them.
Just an aside--with my "86 KX125 i bought new, every new genuine [according to the box] piston kit i fitted would eventually stretch the gudgeon boss of the piston & rattle like mad.
Original piston never did that & i'd refit 'that' if there was a wait for the new kit to arrive, & had to go race in the weekend. Seems crazy but happened each time.
Being a 125 it was on full song from the flag drop pretty much. But eemed like their genuine replacements were made out of cheese lol. Best bike i ever had, that one.
Edit--best Non Yamaha i ever had--get it right lol.