[Mr. Pastorius]

If you're into some heavy combat, two or three guards at the Shi temple are equipped with Gauss Rifles, so, if you're levelled enough, you might consider attacking them. However, you'll turn entire San Francisco hostile, so it may not be such a good idea. Also, when you wander through the mountains, now and then you'll find caves with bandits inside who, depending on your level, may be equipped with Gauss Rifles (at least one of them).
As for the SF gun merchant, he has a restock time of 1-3 weeks, if I recall correctly, so if you don't find the Gauss Rifle on him immediately, come back after a week or two.