1 Meter: HP double > MP double > light Laser Sword > HP double > Shadow Laser Sword > Tiger Fury ender (57%)
2 Meter: HP double > MP double > light Laser Sword > HP double > Shadow Laser Sword > Shadow Tiger Fury ender (62%)
( Damage calculation notes)
Notes: Jago uses his Around the World combo trait; the no-meter variation gets to complete a full cycle, which conveniently does the most damage and builds him 15% of his instinct bar. Shadow Laser Sword is very slow but also much more damaging than shadow Tiger Fury as an ender, so both the 1-meter and 2-meter combos are designed to stick the last two hits past the lockout window to leave as much time for other attacks as possible. If you are in the corner, you can get a 63% 2-meter combo (and 15% instinct gain) as follows: HP double > MP double > LP double > HP double > MP double > Shadow Endokuken > light Endokuken > Shadow Tiger Fury. If you are in instinct, you will have to cancel the light Endokuken after only one hit to prevent a blow out.
Jago only has two special move openers. Laser Sword is a special move that leaves Jago at advantage and should be greatly preferred to Wind Kick when you're at close range (say, for example, after Double Roundhouse or any of Jago's cancelable low attacks like crouching MK). Watch for the distinctive upwards sword swing and voice clip that will distinguish Laser Sword from Jago's normals. In particular, medium Laser Sword is strong, as it hits only once, thus avoiding late shadow counters and still generates a strong +1 on block. Shadow Laser Sword is a high damage opener which cannot be broken, like all openers, so consider using this move often to start all your punish combos.
Wind Kick is quite a bit riskier to use in neutral, since only the light version is safe (at -4), while the medium and heavy versions cover a lot of distance but are always unsafe on block. Importantly, however, Wind Kick is invincible to low attacks, making it a good call out move if your opponent is regularly using a strong low move against you. Medium Wind Kick also has a particular use as a good hit confirm after Jago's long-range Neck Cutter overhead, since Neck Cutter can be canceled extremely late on reaction to your opponent not blocking the overhead. Often, medium Wind Kick is the only non-shadow move that can reach from the tip of Neck Cutter range. Additionally, when in instinct, Jago's increased frame advantage makes medium Wind Kick safe on block, and thus greatly increases its value as a strong mid-range poke from unexpectedly far ranges. In general, however, using any version of Wind Kick, except the short-range light version, without a specific intention to beat your opponent's low moves will get Jago punished. However, Shadow Wind Kick travels very far, very fast, is safe on block and is both low and projectile immune, making shadow Wind Kick one of the best horizontal moves in the game.
If you hit with a close-range Endokuken, you generate enough frame advantage to land a medium or light manual, which will trigger the combo system. Because Endokuken is generally less preferable to Laser Sword as a pressure tool, the main times you will find yourself in this position is if you are also using Endokuken's ability to be charged and dash canceled into Jago's close range pressure. For example, it is a good idea to occasionally mix in charged Endokukens during your pressure strings, since it awards more frame advantage on block. If your opponent is content to block, then vary your offense by dash canceling your Endokuken and perhaps go for a throw; Jago's dash, while short ranged, is quite fast and it will be hard to always keep this situation under control on the defensive end. Changing between semi-charged Endokukens and dash cancels will force your opponent into a difficult decision whether to sit still or not. If any Endokuken hits your opponent, use a manual (or cancel into shadow Wind Kick) to continue your combo. In instinct, the situation only gets better for Jago, since double fireballs improve to only -2 on block, even if not charged at all (where normally they would be punishable). They also generate a ton of shadow meter if blocked, so you are more likely to throw them than dash cancel them, meaning more opportunity to convert stray hits into combos.
Jago's linkers are nice and simple, since they are the same as his openers with no special conditions attached. Laser Sword does more damage than Wind Kick, but the higher strengths are slightly easier to break. If you're fishing for lockouts, medium Wind Kick linker is fast and reliable and still gives you both medium and light manual options. Light Laser Sword linker is his fastest linker and is the best to use if you're looking to squeak damage in during lockout situations. Shadow Laser Sword linker does a ton of damage but takes quite a while to finish, so if you see a lockout and have a bar to spend, try to start shadow Laser Sword after your next auto-double so you can squeeze it in during the lockout time.
Jago has a large assortment of useful enders. His battery ender in particular gains a lot of meter, so you should use it often early in matches, and especially during instinct where all Endokukens also heal Jago. This will give you lots of meter for all of Jago's amazing shadow moves and will make the rest of the fight much easier. He also has access to a wall splat ender for tricky corner mixups, a launcher ender which leads to some solid juggles (and reset potential, using light Laser Sword as a flipout), and an above average damage ender. Shadow Tiger Fury in particular is a great way to finish a round, but I would hang on to the meter if it will not kill your opponent and save the bar for other uses.
Jago does not have a recapture, so he cannot cash out juggle combos without using shadow Tiger Fury. This tends to not be a problem for Jago, however, because he does not rely on air combos that much. The few juggles he does land will come after a launcher ender, meaning the damage has already been cashed out, and you will be finishing your juggles with sweep for a hard knockdown or light Laser Sword, which acts as a flipout. After a Laser Sword launcher ender, hitting with a flipout gives you a good mixup between a frame trap or Neck Cutter overhead. Jago's jumping LP is also a flipout, in case you happen to hit someone with a fast air-to-air attack, but it is not overly important to add to his gameplan.
(Some moves are beyond the limits of human reaction; please read about reaction times to learn more.)
Auto-Doubles: Jago's auto-doubles are fairly easy to distinguish, and he is a good character to choose when practicing combo breaking. Of the reactable doubles, medium punch starts with an elbow to the face, followed with a hit with the blade of his sword; it's the only auto-double to use his sword blade. Heavy punch starts with a very deliberate two-handed strike to the face. Medium kick is animated using the very common close standing MK move, which is a common manual for Jago, so you may see this move a lot. Jago also does the only crouching attack in his auto-double set during MK double. Heavy kick starts with a giant knee to the face. It is common to break heavy auto-doubles with a combination of the exaggerated visual windup, pronounced shout from the character, and the slow, deliberate cadence of the two attacks.
Linkers: You can identify a heavy Wind Kick linker because of Jago's extra loud shout during the first hit, the extra hitstop that takes place, and the small stutter between the first and second hits; these three factors combined should give you enough information to react by the end of the third hit. You can try to break the medium Wind Kick linker by noticing the second hit has taken place without the added hitstop and stutter, but the reaction must be almost unreasonably fast, and it's pretty easy to flinch if the opponent does a light linker instead. Heavy Laser Sword has a similar stutter to the Wind Kick linker; notice that the second hit takes place quite a bit later in the heavy version than in the medium version. It's possible to break the very end of the medium Laser Sword linker if you can quickly identify whether or not this pause happened, but your success rate won't be 100%.
Jago also gets some extra frame advantage after linkers and manuals (specifically, 2 more frames of advantage), which means he can circumvent the manual restriction rules by performing a manual one strength higher than the linker he performed, and he can even freestyle manuals together (such as close MK) mid-combo. These combos give Jago extra options to cause lockouts, which is particularly strong if he is trying to perform a short combo to earn a large cash out, but he's unlikely to use them for long, since ending the combo and using shadow Endokukens to gain health back is generally preferable.
For space control, far standing MP and HP are excellent at taking up space in front of Jago and lead to easy hit confirms off Endokuken or Wind Kick. Crouching MK is a great long-range "shoto-like" low attack, but unlike Street Fighter shotos, you'll probably want to cancel it into Wind Kick or Laser Sword, rather than Endokuken, to maintain better advantage. Neck Cutter (+HP) is a nearly unseeable overhead that reaches three character lengths in front of Jago and should be abused as both a footsies poke and a mixup tool, especially in the corner where you get to control the spacing. Jumping HP is a beastly crossup that can be made very ambiguous and meaty on knocked down opponents.