Don't bother with bolt-on mufflers unless you run accross a set dirt cheap, as they are expensive, instead, look for slip-ons, they do just that, slip on and clamp down to each exit tube at the header.
You'll have Much more mufflers to choose from, including used, and at lower prices.
And as said, no tuning needed.
Putting the brakes back stock?
Lol...don't do that, the stock Gen1 brakes are wooden, garbage, and you definately want the radial mc and calipers that the previous owner put on...which were not cheap either...they are a huge score on a used bike.
For 2nd gear...beat on it, do some hard launches in 1st and high rpm shifts to 2nd. If there is no obvious slipping to 2nd, your good.
You could buy a 100k mile beater and it never slip...or a 1k mile trailer queen...with 2nd slipping badly.
It was luck of the draw to which individual bike had 2nd gear problems, and can only be described as the perfect storm of parts at the factory, one part at one end of spec, or out of spec, mating with another part close to or out of spec.
Not a cheap fix, as the engine has to come out and the case split to get the transmission out, then about $600+ now days to get the gears undercut.
But, after that, the transmission is bullet-proof, and will never have issues again, so worst case scenario, and with a bike that is great otherwise, it is well worth doing...but I wouldn't lose any sleep worrying about it either.
If you find the Busa comfortable to sit on, you will love riding it, and it's not just a straight-line bike either, as you can easily drag knees on it...to which the slip-on mufflers are a great idea, not in just sound and maybe 2hp, lol, but you Can actually feel the weight loss of factory mufflers being gone when flicking the bike side to side through twisty roads.
Carbon fiber mufflers are nice too, as they put the majority of the heat out of the end of the muffler, vs it radiating through the muffler sleeve and putting off even more heat around you.
You can have the bike hot and actually grab and hold a carbon fiber muffler, yes it's hot, but not going to burn you unless you hang on to it for a while, vs aluminum, stainless-steel, or titanium...which of course will give you a 3rd-degree burn in seconds.
The Busa has an endless part and mod list too, and does everything well.
You can make it whatever that you want it to be, and it is already a knee-dragging, straight-line, touring rocket as it is, including being very easy to ride slow, so much so that you can cruise it around all day, think it's pretty fast, but have no idea just how quick it is until you twist it hard...and it'll get up and go.
The Blackbird is a great bike...but the Busa will eat it's lunch, lol
welcome to the org