The Barbarian is known to be a more powerful class than the Swashbuckler. The Barbarian is a so-called "Tier 4" class, the Swashbuckler a "Tier 5" class (see the Tier System for Classes). Parts of the definitions of the involved tiers are "Capable of doing one thing quite well" (Tier 4) and "Capable of doing only one thing, and not necessarily all that well". In fact, the two classes are a particularly good example of the difference between the involved Tiers, since both are primarily melee classes that have a similar "thing" to do in combat - dealing damage. So you really have a textbook example of a power disparity within the 3.5 class system. And this isn't all that easy to fix. Some things you can do:
Tailor some of your encounters to the weak player
Difficult to pull off gracefully, but it can be done. The Swashbuckler has a few things the Barbarian doesn't, including social skills (Diplomacy, Bluff and Sense Motive) and the Tumble skill. The Barbarian having more trouble at a king's ball shouldn't be too difficult to envision. Creating combat encounters where Tumbling plays a huge role is usually an exercise in cleverly positioning enemies (long reach helps) and making said enemies good at taking advantage of Attacks of Opportunity.
Problem is, of course, that it doesn't do much for the problem of the Swashbuckler not being competitive in the damage department. The players would effectively be taking turns at being relevant - not something that ages well in a campaign. But once in a while to keep spirits up should be fine.
A more lasting solution would be to...
Steer the Swashbuckler towards more powerful options
There are a few options that make Swashbuckler more palatable.
Daring Outlaw: Multiclassing and taking the Daring Outlaw feat (from Complete Scoundrel) is a good way to bring a Swashbuckler's damage output up - up and a bit beyond that of a Rogue, at least. This would be my recommended approach if only there weren't a Rogue in the party already. As-is, it might just move the competition from the Barbarian to the Rogue, but perhaps that allows more branching out.
Arcane Stunt: This alternate class feature from Complete Mage grants Swashbucklers a few uses per day of a spell-like ability, at the cost of their Grace. It's a tiny improvement, but usually an improvement.
Factotum: Multiclassing into Factotum (from Dungeonscape) provides immediate extra combat use out of the character's Intelligence. Perhaps more importantly, it can provide considerable utility in the form of skills (and other class features), making the comparison with the Barbarian less direct.
Tome of Battle: Multiclassing or prestige classing into a Tome of Battle class (probably the Warblade for Int synergy) would make the Swashbuckler an enormous lot better, no question. And level 4 is an excellent time to do it (if not before). Problem is, Tome of Battle works for more or less all melee characters - including the Barbarian.
Some Retraining (Player's Handbook 2) may be necessary or beneficial to make the new options fit.
If it won't...
Abandon ship!
The whole situation might not be salvageable. See K.L.'s answer.
a weapon stays poisoned until you critically fail your attack or hit without dealing damage
I'm not seeing the confusion, to be honest. Although mildly contradictory on the surface, you've quoted the relevant rules. By default, an injury poison lasts until the first Strike is made with it. The Fail condition amends the default by saying the poison will remain rather than be expended, although a Critical Fail goes back to the default of expending the poison without effect. Lastly, if you use the weapon to somehow deal damage other than piercing or slashing (either because the weapon only deals Blunt, or through some other effect or special ability), the poison is also expended with no effect on a Hit or Critical Hit. If you somehow had a weapon that could apply different damage types in each strike, and you missed while it was in 'blunt' mode, you could potentially still apply the poison if it hit in slash or pierce mode.
Best Answer
There are two questions I ask myself when approaching this kind of problem.
In what other ways can this advantage be emulated?
If there are any, then these other ways can be referenced to get a basic idea of what advantages you are really granting. If there are no other ways, then you are in unexplored territory and you have to be extra careful.
How well can this character leverage the advantage?
This relies more on your understanding of the character in question, and sometimes of the player as well.
These questions are open eneded because there is no "one size fits all" assessment to determine if something is balanced. Answering these questions meaningfully requires some degree of system mastery, and often involves scanning through the relevant material. Fortunately, 2e.aonprd.com's searchbar makes it relatively easy to find the relevant bits. Either way, assessing balance is difficult on the fly, so when you give out rewards you can say something like "I'll figure out the specifics later".
I can look at your two examples to show you how I would answer those questions.
Gunslinger
Emulation
Using a two-handed weapon with one hand cannot be achieved in other ways.
From here, I would start by comparing a two handed shotgun to a one handed shotgun. Moreover, both shotguns still require two hands to reload, though there are solutions for similar quandaries, such as the Capacity trait or the Dual-Weapon Reload feat.
Overall, the advantage you gave the gunslinger is equivalent to a one-handed shotgun with increased die size, firing range, and scatter range, while also granting her a Dual-Weapon Reload feat that only requires that shotgun. That is a lot to give out, not even a Inventor with Weapon Innovation would be able to improve a shotgun that much.
That said, let's consider emulation from a completely different direction. Both the Core Rulebook and Grand Bazaar have sections written with disabled characters in mind. The relevant bits are a bit scattered, but basically:
A one-armed character can acquire a prosthetic that completely makes up for the missing arm. Only allowing a the Gunslinger to use a two-handed shotgun instead is less powerful than granting her said prosthetic, and therefore unbalanced.
Even so, ruling in the moment that the one-armed Gunslinger could use her weapon of choice to cut the dead fish was the right call, because:
Leverage
The problems start if the Gunslinger gets a new arm or prosthetic while retaining her ability to use a two-handed shotgun one-handed, then she will be able to leverage this advantage: all the benefits of a two-handed weapon build (better damage, traits, etc.), while behaving like a different kind of build. She could keep her hand free to use other items and skill actions, wear a shield, even dualwield two two-handed shotguns...
This isn't something I would personally give out as a reward, at least not without some serious detriment. It's possible that when you say "trained in using the shotgun one-handed" you implied a detriment, because the gunslinger is otherwise expert or better with firearms. An effective -2 penalty might work as a detriment, if the player doesn't find a way to circumvent it.
Bard
Emulation
The Bard could gain the Martial Performance feat via the Multifarious Muse feat. That first level feat would grant him proficiency in all Martial Weapons (including a Cane Pistol), which in the Bard's case means trained from level 1 and expert from level 11. Finding a Cane Pistol in the first place is matter of setting and access, not balance.
However, giving the Bard expertise in a weapon before level 11 is a big no-no. The differing rates at which martials and casters acquire proficiencies is a cornerstone of the PF2e's balance. The only published exception is the Sixth Pillar archetype which has been flagged for errata for that very reason.
Leverage
There isn't much for the Bard to leverage given that the advantage in question is less broad than a level 1 class feat. While the Cane Pistol is interesting, it's balanced compared to other martial weapons, a handful of which every Bard is proficient in by default.