Thank you Marble for the Charlie the Unicorn clip 
A few points based on some of the convos above:
Hisako is not safe jump-able. If she wakes up with counter and you had a meaty physical hit out, you’re getting countered into combo.
The amount of wrath in your meter does not affect the timing, properties, or recovery on counter. It’s always zero frame start-up - that’s why it can be used to catch meaties.
As previously stated, where an attack touches your hurtbox is not relevant to whether or not you counter it high or low. Whether the move is tagged as an overhead or low hit is the relevant determinator for which counter should be used. The 3K counter catching an overhead cross-up would have to be an instinct thing, otherwise it’d be a bug (one that I’ve personally never seen before).
In the instance of getting hit by that cross-up HP through a 3P counter, I can only surmise that the active frames on counter had just barely ended. That’s the only way you should get hit in that situation - otherwise it would have been a bug.
With regards to the main topic, I think the MU is a solid 5-5. Hisako will destroy Jago if she can read him (as she can most characters), but Jago has some pretty good throw setups to work with as well, and his instinct refills can give him a nice chunk of extra health to work with when used properly.
@Marbledecker, I personally prefer to play the fight at very close range (on his knockdown), max-ish Hisako poke range (crouch+MK range), or the extended range you were talking about. I think the middle of these is the “best” neutral spacing, as it puts you into range for dash-up grab and safe-ish pressure. It can be dangerous though, as yolo wind kick at that distance will sail right over crouch+MK and have you eating a combo. If you are playing in that space, it’s good to remember that Hisako far fierce has greater range than cr+MK - that’s important because Jago (or any character really) will be able to move in and out of range of things much more easily than Hisako can. The far fierce will keep them honest once they’ve stepped outside your cr+MK range.
A few of the key things I think to remember in the MU are:
(1) The neutral jump is coming - it’s ok to eat a few throws once you get knocked down. When the neutral jump hits, AA that SOB and regain your momentum. A lot of Hisako’s lose because they’re always committing to something on wakeup - all her options on wakeup are baddish, and leave her in a lot of recovery if she guessed wrong. Learn to be patient and just be prepared to block or get thrown.
(2) Safe jump and cross-up setups off influence ender. Jago is a serious threat if he’s allowed to play. Damage ender is nice, but the Hisako vortex is often preferable in a close fight. Her counter/rekka OS is also a good choice on knockdown. Once he has instinct, I like safe jump into counter - a lot of Jago’s wakeup DP->instinct cancel out of habit once they fill their bar, and this is a good way to punish it.
(3) Sweep low profiles Jago fireball. More importantly, this means that sweep low profiles double roundhouse. When Jago uses fwd+HK and doesn’t wind up within throw range afterwards, there’s a better than even chance that he’s gonna go for another fwd+HK. Simply sweep him out of it.
(4) Use your instinct wisely. If Hisako pops instinct near you, that means you just got combo’d. She can literally turn any situation from Jago standing next to her (except jump+back) into a full combo if she uses her instinct wisely. If they’re hitting you, counter. If they’re standing next to you, light influence. If they’re coming in empty from a jump, use influence of appropriate strength to catch them when they land (as most people won’t jump again, which is what they should do in this situation) - or down+HP->tk air-ORZ them for the recap if you have the time. If they’re trying to throw you, heavy influence them. If someone is next to you when you pop instinct, you should be combo-ing them within the next 2 seconds.
(5) Heavy ORZ’s are very good. Use them to teach your opponent to stop trying to do things in the middle of your rekkas, and then then use that respect to utilize the mix-up options on the next go around. Or just keep spamming heavies…a surprising number of people never figure out that you can’t just always push buttons in the middle of that string.
Those are my not-so-quickish thoughts on the Jago MU. How it turns out is mostly a function of how well you’re able to read and control your opponent’s options.