The 6th edition has the new Jouyou Kanji in it, so you’re fine.
But yeah, don’t do RtK 2. I wouldn’t even recommend doing RtK 3 either: at the stage you’re at, you’re not really going to encounter many of those kanji so it’s not really a worthwhile endeavour.

I’d say the method you’re using is fine, just a little slow. Either cut it down to writing the kanji only 3 times, or use Anki to “Cram” them (goddamnit, I wish there was a sticky thread so I didn’t have to keep explaining this and everything else >.Cram, go through the list a couple of times, clicking “Soon” each time so that it will show the card again. Not very good if you like keeping your Anki stats high, but they don’t really matter, right? If you’re really bothered about stats, just make a duplicate deck to Cram with. You shouldn’t need to do so much repetition at the start since that’s what Anki is for.

You should aim to do more kanji/day as you get better at it. Use kanji.koohii.com for stories since Heisig’s are a little… rubbish most of the time haha.

Also, I’d really recommend using Koohii for keyword->kanji flashcards and Anki for kanji->keyword flashcards – doing it both ways (giggidy) really helps with remembering them.

Cramming and two-way review are two things I wish I had done from the start. Try them out :)

Sheepy, if you’re reading this, get that goddamn sticky thread going! Or Cassandra! XD