This is the boss notes. Due to the size of the description - I couldn't include this within the description itself.

Marble Garden:

Drill Mobile (Sonic's Version):
This requires debug mode to access. Since Knuckles cannot jump very high he must fight it in the usual "method".
Tails thankfully appears like he does when playing as Sonic. His glide move makes getting extra hits easier.

Carnival Night:

Graviton Mobile:
Oooh boy, one of the big "missing ones". It's actually possible to enter the boss room via a glitch in stage design, but it's easier to use Debug.
Initially, this fight looks to be a very long, very boring battle, as Knuckles can only get a single hit on the machine as it lowers and rises.

HOW-EVER! It turns out that the mech is vulnerable from BENEATH. It's almost pixel perfect requirements to hit him, but it cuts the time fighting this thing down by minutes.

Thanks to Joe Collins for informing me!

Launch Base:

Twin Hammer (Sonic's Version):
Oh boy. This took FAR too much effort to get. Let me explain:

You need to enter the stage as Sonic, activating the "play as Knuckles code" afterwards, but also having the "Sonic Character ID Code" activated.
When you reach the boss starpost, you need to enter a bonus stage, which, when you leave, will let you jump out as Knuckles.
If you've got the Sonic Character ID Code activate, the boss should appear, although Robotnik will not.

The game then proceeds to lock up when you beat it. Basically, you have to break the game to fight this boss as Knuckles.
Emulation was really helpful in this instance. This wouldn't be possible on a console.

Ball Shooter:
Getting to this boss is easy with Debug. But... rather oddly, this boss cannot be defeated by Knuckles without a PAR code activated.
No really.
Go on.
Try it yourself.

Can't beat it via normal playing? Yep. For what-ever reason, having the Sonic Character ID code activated allows Knuckles to hit this boss, albeit only by gliding.
The fight is still glitchy as hell, (as shown by me bouncing all over the play) but at least it's fightable.

Lava Reef:

Hot Mobile:
This fight is accessed via the Stage Select (Hint, it's Lava Reef's Act 3). I will be showing this fight in the Video Response, as it lasts so long, I couldn't fit it in this video.

Hidden Palace:

Knuckles:
Wait.. what? Yes, you can fight Knuckles, as Knuckles! It requires a specific Game Genie code to load this boss.
The cutscene afterwards is also messed up, but that will be shown in the video response.

Sky Sanctuary (Sonic's Version):
Just choose Sky Sanctuary Act 1 on the Level Select. No other codes required. You DO get to see two Knuckles' working together at the start of the level.

Green Hill Boss:
It's the boss from Green Hill! Nothing much to see here.

Metropolis Boss:
What was originally a piss easy boss for Sonic, is rather frustrating as Knuckles. (No Sub-Spin)
If this was identical to the Sonic 2 version, there wouldn't be a problem.

But apparently, the entire boss was re-coded, and is now much, much harder to hit. The timing takes a while to learn, but it's doable.

Mecha Sonic (Sonic's Version):
Almost the same as the Knuckles fight, but there is one or two changes to the AI. Also, I managed to glitch it up here. Hah.

Death Egg:

Red Eye:
Ok. This is the major one here - Knuckles cannot in any way shape or form defeat this boss. Even ABUSING Debug mode, it's difficult to do.

This is where Rom Hacking comes into play! I added a wall to the battle (thus meaning it's shield of orbs is still a threat, as are the spike spreads it fires as you take down it's defences. This is STILL the hardest boss in the game, by far - and that quick kill is tough to pull off.

It basically involves you hopping from one "side" of the boss to the other, attempting to get it's spiked platforms to balance out - you then need to land in the centre of the boss and it should die before it does anything.

Death Ball:
My strategy as usual, involves waiting for a good opportunity to spin dash into the spiked badniks. No real "changes" when you fight this as any character.

Kyodai Eggman Robo:
Yes, that is it's offical name.
Knuckles has a fairly easy time against this boss, as his glide combined with good timing allows you to score four hits every time Robotnik opens his Emerald Laser.
Still, the boss is epic, so you can forgive this being a easier than usual Sonic final boss.