I have limited knowledge of Mortal Kombat. But there is a few things that I do know, and part of it is due to
the SNES Publication.
Bicycle Kick is the most effective move in Mortal Kombat II.
However it's not the fastest in quickly ending a round, a mid kick, two quick jabs, anything to get the character to celebrate quickly is more effective.
In your input you are holding your input down for Bicycle Kick which is fine.
However, this leads to problems such as with the Jax fight where you don't attack for a few visible frames.
So you can't say that you're being optimal there, when visibly you're not. This is something that can be avoided if you used TAStudio effectively to clean up your input.
Look at the input to
the SNES Publication if you want a better understanding about how to clean up your input.
Taking any form of chip damage with a block is faster than having a "Flawless Victory" (Perfect Round) as there is less information the game gives you bringing down the time.
There is a way to lightly manipulate the AI to give you an attack you want from them that you can effectively block (preferably a projectile), since the TAS is on Medium it's a bit harder.
Obviously for the final round with Shao Kahn go for "Flawless Victory" because you're ending input as quickly as you can here.
Another thing that can be done is change the Sync Settings on the Arcade dip-switches settings.
Change
Coinage Source to "Dipswitch" then
Coinage from USA-1 to USA-Free Play this will give you some free frames.
It's a good start but there's more that can be done.
Please take your time and use the tools available to you in BizHawk and
use the userfiles.