First, it seems that digifish has provided the definitive aswer to your questions above, so I'm not all that sure I can add much.
I'm not a nature recordist, but as I was initially reading through the responses this morning I was thinking along the same lines as digifish about the fact that all the talk about the recording device is somewhat misplaced discussion unless you did want an all-in-one device. The point being, as digifish said, you've already got exactly what you want/need for field recording...a good mic and a tiny portable high quality pocket digital recorder. All you need to add is the high quality low noise pre-amp to get your gain up!
Obviously, if you wanna go with an all-in-one, you don't have to worry about buying the high quality, low noise preamp because it will already be a part of the all-in-one recorder! Just make sure you're dealing with either Busman or Oade when you get your all-in-one (if you go that route) because they'll best be able to tell you what products they have that would suit your needs!
Not sure if this is your issue, but regarding the clicking sound, be aware that on the early R-09s that were delivered a couple of years ago, the line-in jack had a really weak connection where the jack was just basically connected to the PC board with a dollup of solder...this broke for lots and lots of people. This connection needed to be beefed up (under warranty by Edirol or I sent mine out to someone here on
TS.com) so that it could withstand the plugging and unplugging over time by first fixing that solder connection and then securing the jack with a glob of epoxy in order for that jack to hold up to the rigors of the field. Yours might be coming loose!
EDIT TO ADD: Some people resolved the above connection problem by adding another short cable to their R-09 and then leaving that cable permanently affixed to the R-09 in order to minimize stressing the line in connection, while plugging and unplugging from the female connector on the cable instead of the R-09. In my case, after I'd had my R-09 repaired, I bought a short cable and then wrapped a velcro strap around my R-09 so that this extra cable was secured to the body of the R-09 (and so that the cable couldn't be pulled and yanked thereby stressing the line-in jack anymore) and I just plugged and unplugged from the external cable. Not an ideal situation, but workable and solved the problem.