I was reading in a home defense mag that you shouldn't handload self defense ammo. There is no way to prove what kind of load you used, and by the pattern of gun shot residue there is no way to prove what distance you shot from if you end up in court. Seems to make sense to me.
That sounds a bit crazy to me... but I didn't read the article either. It shouldn't matter what sort of load you're using, it's not like you're going to load some +++P rounds and shoot someone breaking into a home three blocks down with a .45 pistol. Could such a thing be done? Probably. But I wouldn't advocate it.
As far as gun selection goes...
A shotgun makes a great equalizer, but as has been pointed out, it's not really a good weapon to be hiking through the house in search of an intruder with. Sure, you can put a folding stock on it and an 18" barrel, but it's still a long gun. If you're walking past a doorway and an intruder jumps out, it's still long enough that he can push it out of the way. That's why the recommend that if you do clear a house, a good way is with a pistol held tight against your side. That sort of grip is real hard to deflect and the gun can be quickly brought up to use the sights if a longer range is needed.
A shotgun is a good "barricade in the bedroom" type weapon. As in close the door, lock it, get down behind the bed with the shotgun leveled at the door and call the police. If the criminal kicks in the door, you blow him back out it.
I would not recommend "clearing" a house unless you've been properly trained in it.
The .45 auto has gotten a bit of a bad rap. Some people may find it difficult to control, especially in the old 1911 style. In the past few years I've gotten to shoot quite a few different handguns and I've been surprised by some of them. Just two weeks ago I got to shoot a Sig in .40 cal along with some other brand of .40 cal. I also got to shoot a 9mm Taurus (looks like the Beretta 92) and a Springfield XD-45 Compact. Surprisingly enough, the 9mm being the largest, it was almost as bad as the .40 cal pistols for recoil and muzzle flip. The .45 was the hands-down most comfortable to shoot, recoil and muzzle flip was no worse than the 9mm. In the past, I've also shot 1911 .45 pistols, a total titanium Taurus snub in .38, a Bersa .380, and a Taurus Raging Bull in .44 mag. The lightweight lil snubby wasn't all that bad to handle, no worse than the Bersa in my opinion. And the Raging Bull surprised the hell out of me, I expected serious recoil, but found it easier to control than a .45 auto. My buddy's girlfriend even got talked into trying it and was surprised to find that she could control it easily. The only problem was that it's a heavy gun (the owner uses it for deer hunting).