I was in a similar situation; I took Japanese classes after a few months of starting RTK, and concentrated on my "Japanese Classes" deck rather than my Heisig deck for six months. That left me with 800+ cards due! Eek! And the cards that showed up whenever I opened up iAnki were ones I didn't remember, and I could never get through a session with (what felt like) more than one or two successes.
What I ended up doing was effectively starting from scratch using this site's web SRS, while still plugging away at iAnki. Using Koohii helped my motivation because it showed me cards that I did remember, so I didn't feel like I'd been wasting my time. It gave me lots of successes, which always helps motivation. I could do a whole lesson's worth of Kanji at a time and remember a good chunk of them. It really felt good, and got me back into the joy of Kanji!
Meanwhile, I was chipping away at my Heisig deck on my iPod. Because I do all my reps on my iPod, it's easy to find a few minutes here and there (waiting for the bus, on the subway, etc.) to do some reps. Eventually, I broke through the wall of cards I couldn't remember (presumably they were the last ones I had added before the 6-month break) through to the ones that I could. Things became easier and easier, and I could go through dozens of due kanji in a day, split between three or four sessions of what would otherwise be "dead" time. Once I got a good grip on my iAnki deck, I stopped using RevTK.
It took several weeks, but I eventually got that 800 card monster all the way down to zero, and now most days I completely finish my kanji reps. The only days I don't are Mondays, because I forget iAnki on the weekends!
I'm now working on getting my Japanese Classes deck in hand, too, but it comes fourth after Heisg, Hiragana and Katakana. And I'm going to make sure I keep it that way, even if I take classes again this year.