The first jump does NOT count toward your total. It will look like 101 jumps but only counts as 100. The game forces you to stop at 100.
The frame window for landing the jump gets progressively smaller until you hit 13 jumps. After the 13th jump, the remaining jumps all have a 3 frame (1/20 of a second) window to land.
(The input window ENDS at the same time for all 100 jumps, but BEGINS at a different frame for the first 13 jumps.)
If you are trying this technique on an emulator, good luck. Missed super jumps on emulators are more common due to inconsistent frame rates.
If you drop jumps in a battle where Super Jumps are used only for damage output and not for the reward of Super Suit (such as Boomer, Earthlink, Smithy, etc), you can usually just do Super Jumps again to make up however many you had left. When you start Super Jumps the second time, remember that the first jump every time you initiate the jumps does not count toward your total. The uncounted first jump also does the damage output equivalent of 8 super jumps. That means if you need to do 47 super jumps, but you drop at 20 and had 27 remaining, your next round of jumps should be going for 19, not 27.
You must get 100 Super Jumps at least once in Peach Chart as the Super Suit is required, ideally in the Johnny fight. However, dropping jumps on Johnny is not a run-killer (unless you're trying to PB and losing time from dropping). You can attempt Super Jumps as many times as you want in a run, it does not matter which enemy you get them on.
Once you figure out the rhythm, keeping it is entirely a mental task. How you maintain your consistency is up to you. SMRPG runners have all sorts of weird placebos that help them mentally with keeping the rhythm, and discovering yours is half the battle. When starting out, you may struggle with things like: having your rhythm thrown off by blinking, eye irritation from not blinking, anxiety over losing count of your jumps, tension and nervousness while hitting higher jump counts, second-guessing yourself during jumps, early rushed button presses out of excitement when close to 100, and mistimed presses out of frustration with learning the technique. All of this is completely normal and common, and you will overcome it with practice. Remember, if you get 14 or more, you've already figured out the frame window once, so you know how to get 100.
Do not expect to be good at this trick right away, yes that means you, even if you're a musician! Please do not go into learning this trick expecting to be above average at it right away because of other experiences you may have in your life or with other games. You may end up being good at it right away, you may not, it varies from person to person with no real pattern or common factor. Keep your expectations low, so that you will be encouraged by your gradual success, instead of being discouraged by not meeting a standard you may have set for yourself before even trying it. One of the biggest hurdles with super jumping is how demoralizing it can be, so mitigate that as much as possible by not making assumptions about how good you should be at it after an arbitrary amount of time. It will come to you with practice, I promise! Keep practicing, you will be consistent! But remember to take breaks, they help.
I usually recommend to practice super jumps in intervals of 15-30 minutes at most. After that time passes, take a break to practice other important tech like Mack Skip or area movement and timed hits, or anything that you've had moderate success with. Then you will be in a good mindset to get back to the super jump grind.
You can use any of the A, B, Y, or X buttons to do Super Jumps. Pick whichever you're comfortable with.
It is not recommended to attempt Super Jumps with Jump Shoes equipped. The animation looks very different: Mario spins in a way that is distracting and provides an inconsistent visual cue. This stops when you remove the Jump Shoes. It is widely believed that you will not get the Attack Scarf or Super Suit if you perform the jumps with Jump Shoes on, however this is not true (proof). It is just simply not recommended for the stated reason.
(starts at around 23:10)
The following battles use Super Jumps:
Johnny (100 - required for Super Suit. He will die if you drop at 95 or higher)
Belome 2 (100 if you missed 100 on Johnny, 57-59 otherwise depending on Geno attack damage RNG)
Jagger (optional fight -- get 100 here if you missed 100 on Johnny and Belome, then run away)
Czar Dragon (24 if you have 1 ice bomb, 42-43 otherwise depending on damage rolls)
If you have 2 ice bombs, you do not use Super Jumps.
Machine Made Yaridovich (20 if you freebied a Rock Candy, 25 otherwise)
NOTE: The time window between SJs is slightly longer for Earthlink and the rhythm will be marginally slower.
Smithy 1 (69-71 depending on Mario attack damage RNG)
Optimal: 100 on turn 2, rest depends on your choice of strategy