This pertains to X-Wing SE...

Tour 5 Op 14B:

I have identified and disabled the correct enemy transport, destroyed all opposition, and am waiting for the ‘capture’ transport to arrive. How do I finish the mission?

I recall one mission where I destroyed a shuttle trying to capture an X-Wing, but then a new shuttle arrives... and another after that. So there is most definitely a function for this.

Tour 5 Op 15:

How do I switch over from an A-Wing to one of the B-Wings? I cannot complete this mission when all the B-Wing AI’s all let themselves be killed. I’m far better off simply doing the whole mission using just ONE B-wing than playing the role of escort to a bunch of stupid AI’s.

I've chosen General-level pilots for those B-wings... they also let themselves be killed or captured, just like the standard AI's.

General Question:

How do I lock a missile or torpedo onto a target w/out disabling my cannons? I have kept the target in my sight for well over ten seconds and then switched over to the missile/torpedo... only for it to fire stupid as if it weren't trying to lock on at all. Given that enemy TIE bombers and Assault Gunboats consistently fire their cannons while locking on, there is definitely a means to accomplish this.

If the DOS version try slowing down the cpu cycles in DOSbox.

The exact same problem happened again! This time it's tour 1, operation 8.

I have identified and disabled the transports carrying prisoners, that second transport doesn't come in and do its ******* job. I managed to destroy both frigates and all their fighter complements. A spectacular victory! Then I hyperdrive out and the next screen lies... MISSION FAIURE!!!

How was I supposed to have summoned a new transport to complete the mission?

I just played T1:OP 8 again to see what went wrong and I couldn't believe how badly designed this mission was! The reason that the transports failed to do their job is because I had disabled a transport filled with troopers and one of the 'rescue' transports boarded that one instead!

At this point I shouldn't be outraged. This was a badly-designed game from the start. I wish that gog had adapted a more modern version of this game for Apple, because I would use that version and never give this a second thought.

The AI routines had hard limits and they kept them for all subsequent versions to avoid breaking anything in the porting process to new engines and operating systems.
They did correct most of the issues with Tie Fighter and while there are still some script glitches here and there in some of the most complex missions towards the end of the CD version campaign (which had an additional expansion that concluded the story).

Also do keep in mind that this is a thing you won't notice unless you disable transports willy-nilly, for example I never knew of this quirk of the engine because I never wasted ions on anything that wasn't something the briefing told me I had to capture (or a shieldless Star Destroyer/Corvette/Frigate).