Well, counselor, I have some observations based upon some 30 years as a detective having been assigned to the Major Crimes Division which, as you guessed, includes homicides. I am not an attorney so this is in no way legal advise.
As you say, the defendant at bar in criminal court, bears no burden of proof and can sit back with a "prove it" attitude. However, an affirmative defense, as you well know, is required when certain defenses are going to be employed. Under a (FL) "castle doctrine" or "stand your ground" defense, the defendant not only must take the stand and testify, but must appear and testify before the judge in a bench trial (no jury) to satisfy the question (and elements) that the shooting was good. And if the defendant can convince the judge, there will be no criminal trial before a jury. Case closed. However, if not successful, the case is bound over to criminal court for trial. And, at trial, the defendant can again use the defenses brought at the bench trial to convince his jurymen.
From where this misinformation comes that you will not get your firearm returned to you if it is taken in as evidence is beyond me. Frequently, at bench trial or upon acquittal by jury, the judge orders all property, including the firearm, to be returned to the defendant. In other words, I don't know anything about carrying a Bar B Q gun for EDC, but I would use a gun of a quality and reliability you're willing to stake your life on. Don't cheap out on something like that. And even if true (although its not) the best gun made is likely going to come thru when needed most and if it saves your life it earned its keep. Let 'em keep it. Buy yourself another one.
The criminal v. civil arena. It has been my experience, merely as a witness but also having been qualified and testified as an expert witness that the truth is more often gotten to in civil court as opposed to criminal court. Less procedural rules barring evidence and kinds of evidence and a lot more latitude given to the lawyers in both discovery and what the judge will allow in at trial.
Weapons modifications. Well, of course, if the case is sent for criminal trial these things will be brought out. If the preliminary hearing judge is satisfied it is a case of self-defense and a good shoot this is a non-issue. But at trial it will loom large. Some modifications are helpful. White light on accessory rail; plastic sights replaced with steel night sights. Others not so much. Exotic hand loads that explode upon impact or are body-armor piercing; trigger mods.
I agree with someone above that said keep it as stock as possible.