Flashing a kernel is the same as flashing a rom. You put the rom zip and the kernel zip on sdcard. I personally always use the external sd but thats me.
Traditionally, a wipe (factory reset) wipes the /data partition (and /cache) only. This is where your apps, settings and data is stored. It doesn't touch any required parts such as ROM, radio, kernel, recovery, boot, dpownload mode etc.
On the s3, the FUSER file system places /data and /sdcard in the same space so a wipe via android wipes both. However, you never use this method once rooted. Wipes are done via recovery now and /sdcard is no longer wiped.
As for GAPPS, if you're on a 4.1.2 ROM, flash 4.1.2 GAPPS. Theres no difference between the one in the CM threads and the one in others.
One step at a time. Theres will be mods for 4.2 stuff, but baby steps please. Root first. Then ROM. THEN mods.
In regards to the developer, his stuff is more his than ever. My (presently muted) views of immoral conduct are based on evidence witnessed on older "works". Until I have ascertained which AF rule I have broken that brought about the censorship, I wont discuss that any further in the open.