Memorize Master Core's attack patterns. Having just beaten it at 9.0, I'll tell you that the first thing you want to do is memorize Master Core's attack patterns so you can dodge. I'll tell you my strategies for each part of the fight:
Master and Crazy Hand:
Attack them as much as you can without taking much damage yourself. If you're over 60% going into the Master Core fight, you're more than likely screwed, unless you can clutch like crazy.
Master Core Giant:
Blitz the ******. Seriously, kill him as fast as possible. Master Core Giant is by far the most dangerous Master Core form, and the faster he's gone, the better. Memorize his attack patterns and dodge at the right times to minimize damage.
Master Core Beast:
Play Defense. Hit and Run. Master Core Beast doesn't exactly have a set attack pattern, so what you should do is wait until Master Core Beast attacks, then attack it with a quick Dash Attack, Tilt, or if you're feeling lucky, a Smash Attack. Watch out for the spike attack, as it can go right through shields. If you get caught in the lightning attack, Shield. The lightning doesn't do much damage to a shield, and once the attack is over you can counter-attack. Repeat until dead.
Master Swords:
Revert to Hands Strategy. Dodge as much as you can and attack frequently. If you die on this form, you're doing well, so don't worry. Make sure you pick a character with good air game, as without a good air game this form will take a lot longer than it should. When the swords split up and attack you from all sides of the stage, dodge the first four blades from the side, and then shield the final blade from the top. You can then use a quick Smash Attack for extra damage. Other than that, chip away at it with Aerial Attacks.
Master Clone:
I don't have much to say about Master Clone. I was using Marth, so it was relatively easy for me. Stake out the center of the stage while he's materializing, and then counter when he attacks from the air. From there, keep him off the stage. Make sure you don't don't give Master Clone time to attack. Disrupt his every move and keep him off the stage. Remember that in the beginning of the fight he's going to have bigger hitboxes due to his bigger size. This is both an advantage and a disadvantage. On one hand, he's easy to hit. On the other, his attacks have longer range, so be aware of that. I would think attacks like Ness' PK Fire and Robin's Arcfire would be good to spam to make sure Master Clone doesn't move, but I don't know.
Master Fortress:
Ah Master Fortress. You're like Smash Run from Hell. I had a tough time with Master Fortress too, so don't fret. Here's what I did. First thing's first, avoid the Stalfos. They're annoying and not worth fighting. When they attack, they have a cooldown period when they won't attack, so use that to your advantage and move past them. TAKE OUT THE FLOWER CANNONS AT ALL COST. They are deadly and can ruin a perfectly good run. If you see one, murder it. I'd also advise you to do the same to the Plasma Wisps, as they can be fatal too. Don't worry so much about the little bugs on the ground, but do know that they have spike properties, so don't touch them, and kill them if possible. When you find each of the four cores, make sure there are no enemies around it. Master Fortress Cores 2 and 4 both have enemies that spawn once you hit them, so be aware of that. Also be aware of the fact that the same enemies spawn in the same places every time, so use that to your advantage. Be extremely careful of those yellow danger zones. Don't fall into them. As stupid as it may sound. I had a run where I caused 72% to myself just off of being stupid and touching those danger zones. That's why you need to kill every ranged enemy, as they can knock you right into a danger zone. This is especially true of Core 4, but as long as you take out the enemies that spawn there, you should be fine. Hack away at the Cores with as much power as you can.
Master Core Core:
Beat the everloving **** out of it for all the trouble it's caused you.
General Tips:
-As each form of Master Core is assembling, charge a Smash Attack so you unleash it right as the form materializes. The extra damage helps in the long run.
-Use your shield liberally. It's very useful.
-If you somehow manage to make it to Master Fortress with two lives, you're pretty much golden (That's how I ended up in my winning run)
-If you lose, don't bother with 8.5, it isn't worth it.
-Know that it's gonna take a while to get that one run. It probably took me over 20 tries to beat it on 9.0. There were plenty of times where I killed on the way to the boss fight or in the boss fight itself. Don't be disheartened by loss. Use it to make you stronger. If you start getting angry and agitated at the game, take a break from Classic Mode. Go play some Smash Tour or Orders Mode, or just take a break from the game until you're in a clearer state of mind.
-Don't let your nerves get the best of you. Don't focus on the timer in the upper righthand corner of the screen. You'll have more than enough time to fight Master Core and defeat the Master Fortress. Don't rush and go HAM on any of the forms, especially beast. Then you find yourself at over 100% on your final life. And then you lose. Take your time.
Other than that, not much I can think of. Might I ask what character you're using, and the strategies you're using as that character?