I don't see exhaust burnt out--i mean Really Burnt Out--its the 'Main Thing' that robs 2strokes of performance.
Tail end muffler [complete tail muffler] is more likely than the main exhaust but still pays to do it all. In the bonfire overnight. Of course i could be very wrong haha. I was wrong once--i think!!.

The Carb rebuild with a Keyster kit rings alarm bells with me .
There have been many instances here , when new members have purchased rebuild kits , only to find their bike runs like s**t .
The needles especially often bear little resemblance to the Mikuni item they are touted to replace .
The jets themselves can be hit and miss components too . You're much better to use genuine Mikuni parts , either from a Mikuni
parts supplier or OEM Yamaha .

Yes, 1000x yes on what Swoop said on Keyster and using genuine Mikuni calibrated parts.

Its often difficult/impossible to get genuine Yamaha parts to rebuild an OE carb. In the case of things like main and pilot jets, the parts will be available from someone like Sudco off the shelf.

However, other parts like needles and needle jets are in many cases manufacturer specific, and in most cases are not likely to be easy to find.

Before anything else, fit the original parts back in the carb and see if that improves running. Also has the timing been properly checked?

Thanks to all who answered.

After some inspection, I noticed the needle that came with the jet kit is indeed wrong. It appears that most carb kits use the needle meant for the DT400. I ordered a 6F9 needle and now I can hit 75mph with no problem.

I've also got some OEM Yamaha jets on order, they'll just take awhile longer to arrive.

Mikuni was the OEM and often parts like the slide needle, needle jet, pilot jet, main jet, and float needle/set are cheaper from a Mikuni distributor than going through Yamaha... if Yamaha even still shows them... (Many Mikuni parts no longer sold by Yamaha are still readily available from Mikuni)