Speed equalization.
This is to me more like an "Endure" pokémon move which boosts durability until every single attack causes only scratch damage. Given Link is "higher" than his base with equipment and can use this on top of that, he should at least be able to reduce Cloud's damages to a tolerable amount, especially since this skill works against cutting and piercing attacks versus skin, not just blunt damage which is the kind the human body best resists to.
If that's the case, he should be able to survive attacks and fight on equal footing for as long as this lasts by stacking this atop his best equipment. If his shield can defend even a single blow without breaking, it can regenerate back into full health and that allows Link to tank even more attacks.
However, can Link damage his opponent? This is what will truly decide the battle. If he can, then this is no longer a stomp and all AP-based votes might as well get refuted.
I'm now reading his page for magic and such, and it seems Link has many ways of becoming invulnerable. Add that to his extremely high stamina and yes, he can survive being struck by Cloud's "one thousand times stronger" attacks at least a couple times with his own body, his shield should be able to tank one blow and regenerate (Skyward Sword), allowing him to further not be trash. He can also use Life to heal himself and use the Purple Potion to ressurrect. Same does Fairy, Great Fairy's Tears can double his AP. There is also Bear Minimum which allows him to dodge attacks, but he should get one-shot should it fail, given it doubles damage taken.
Master Sword can deny Cloud's Regenerationn... The Fierce Deity sword should give him the best AP. Stack every single attack and defense and invulnerability boost he has or at least have one defense+invulnerability boost at all times, use the shield but focus on dodging... and he should be able to face Cloud.
Link has gifted levels of ability with problem-solving and fighting, plus much more experience than Cloud. I give this to him, yeah.
One thousand times difference or whatever, my vote goes to Link.