software

I LOVE Slash's neck tone, so the obvious choice would be the APH in the neck. However I've heard amazing things about the Pearly Gates, and according to the chart they seem relatively similar. Can I get that same Slash smoothness and sweetness as well as the good cleans in a PG? Which would you guys suggest? I don't need to NAIL his tone, it's just that overall style of creaminess that I'm going for, and they're both Alnico II.

If you're going with a high output bridge pickup, I think the PGb model would do well in the neck for what you want it to do.

Both are nice pickups, no doubt about that.
To my ears, the PG is a bit smoother and not as glassy as the a2pro. You have to pluck the strings a little harder if you want the notes to jump out. At the same time, I think the PG's tone is a little more complex in the mid frequencies.
I prefer the a2pro, just because it seems to work with my style better than other humbuckers.

One thing about slash's tone that is widely overlooked but very important is his picking dynamics and the sound of his pick attack. The A2P's have such a sweet attack so your playing doesnt sound like just plain notes.