Homing Missiles are a waste if you've got a Heavy Laser Cannon because HLC will ensure you always roll 4 attack dice at enemies in your forward arc anyway. These are especially useless if you're playing against Rebels, because only the A-Wing (or Falcon upgrade) is capable of evading.
The Gunner could also probably go. With 4 attack dice, you're not going to miss often enough (especially against X-Wings and Y-Wings) to make this upgrade worth it's weight in squad points.
If you insist on running Boba Fett alone, I would probably go with
Boba Fett (39)
Veteran Instincts (1)
Cluster Missiles (4)
Engine Upgrade (4)
Mercenary Copilot (2)
Seismic Charges (2)
Heavy Laser Cannon (7)
The rationale here is that Veteran Instincts will ensure that Boba always maneuvers last - this will let you get the most out of his pilot ability and also let you decide if the time is right to Boost (since you've also got Engine Upgrade) or to drop your Seismic Charges. Don't hesitate to Boost past your foes and catch them in your rear arc. The HLC will be useful at long range, and you'll also have your Mercenary Copilot to help you out at this range. If you happen to catch an enemy in your Range 1 forward arc, hit them with the Cluster Missiles - these are especially well-suited to tearing up Y-Wings.
Both of your statements concerning Homing Missles and Gunner are clearly misguided…
The only thing i like in your build is the boost and veteran instincts, those are well thought out upgrades
To weigh in on this, I wouldn't bother with the Mercenary Copilot if you're running the Heavy Laser Cannon. The Mercenary turns a hit to a critical, but the Laser Cannon downgrades your criticals to regular hits, which, if I'm remembering the rules correctly, you always go with the "worse" option, which in this case is the critical turns back to a regular hit.
At Range 2 and 3, you're obviously going to opt in to the Heavy Laser Cannon for the extra attack dice, especially at Range 3, because your opponent won't get the extra defense dice, as doesn't apply to secondary weapon attacks.
The Gunner would be a better crew person choice, and I think I may have inferred that it's not fully understood how it works. So let's say I'm using the Heavy Laser Cannon (HLC) at Range 3 to attack you. I roll it up, and my end result is 2 hits. You roll your green dice and get two evades. The attack is considered to have missed, because no hits were scored, so the Gunner's ability triggers, and you can roll a Primary Attack with your 3 reds and hope you get lucky.
It seems that some people assume the Gunner or Luke only work if your attack dice rolled zero hits, which is false. You could roll 4 hits, but they don't count as having "hit" until your opponent has rolled and resolved their green dice, including modifying results with Focus, adding in their Evade token, using Elusiveness, etc. If the final net result is that you have "hit" or "critical hit" dice results on the table, and they have all been cancelled by Evade results, Evade tokens, or other abilities, and your net "hit" and "critical hit" count is zero, you have missed. Then your Gunner or Luke can activate to try and roll again.
Hopefully that made sense.
Now, getting back on to the original query, regarding Boba Fett, here are a few considerations for your Firespray pilots;
Fett can work well with anything that also adds on to his movement, with things like Engine Upgrade to perform the Boost action. Since you can alter the movement dial to the opposite bank move after you reveal, the Boost can help those correcting moves to keep good firing solutions for Fett's two fire arcs. Veteran Instincts also moves him up to a Pilot Skill of 10, so you can have a better chance of moving last and taking advantage of that for Fett's ability.
Kath's ability works well if you take the Slave I upgrade and Proton Torpedos, which ups your critical hit chance. Consider also a combination of that, Marksmanship and Mercenary Copilot, which all let you add crits to your die roll. You get an all win outcome; if the crit is absorbed by a shield that's one less shield. If it goes through to hull, they take a face up card. If they cancel it out with Evade dice and tokens, they get stressed, which can potentially mess up their movement next turn. If you can team her up with a Bounty Hunter and Ion Cannon, you could potentially shut down a Small ship for a turn, but that's probably too much of a points investment to deal with one fighter.
Krassis works great with your secondary weapons, so be sure to take along the HLC, Ion Cannon, or even go all in and take Slave I and Proton Torpedos. At the very least though, use him with the HLC or Ion Cannon, sprinkle in the Torpedo if you have 4 points to spend. Combine with the Mercenary Copilot to increase your Range 3 crit potential, or the Gunner for a do-over with the primary weapon if they stop your secondary attack.
The Bounty Hunter doesn't have a specific pilot ability to work with, so I would relegate it to a support ship role, using some of the above combos, or even as a mine layer. I haven't done anything with the Bounty Hunter yet, so if anyone has any experience using it successfully, I'd love to hear more.
The best thing to do, honestly, is really consider the implications of those Pilot abilities, and try and chose a load out that lets you exploit that the most.