Welcome back to the world of video editing! With Final Cut Studio 2, you should be able to edit almost any file type as long as you convert it into a ProRes QuickTime file so that Final Cut Pro can easily read and recognize it. Some file types may not work with Compressor or Final Cut Pro's Log and Transfer. A list of supported codecs can be found under "Specifications" on B and H's page here: http://www.bhphotovideo.com/c/product/492017-REG/Apple_MA886Z_A_Final_Cut_Studio_2.html. Those are codecs you can hopefully find when picking out your camera.
Also, don't forget that many camcorders now come with software that will help you to convert your footage into other popular formats for use in editing software like Final Cut Pro.
As for the camcorder itself, I would recommend using something like the Sony NEX-VG30: http://store.sony.com/p/Sony-NEX-VG30-Interchangeable-Lens-HD-Camcorder/en/p/NEXVG30. I know that it isn't an HDV camera, but going away from tape has a lot of advantages! If you're worried about archiving, a good, high-capacity RAID can accomplish the same means as tape. In addition, a Blu-Ray archiving system works just as well, albeit a bit slower. The VG30 has a nice microphone, interchangeable lenses, a huge sensor, a verylong zoom, and best of all – hits your price point with an 80-200mm lens at $2,049.
The one downside is that the camera doesn't include an XLR port. It does, however, include an 1/8th inch audio port which can still be used for shotgun microphones that are powered by an external battery. If you want to use a shotgun microphone that needs phantom power from an XLR port, I would suggest using Sennheiser's G3 wireless system with an XLR adapter that gives phantom power like this one here: http://www.bhphotovideo.com/c/product/618735-REG/Sennheiser_EW_100_ENG_G3_A_Evolution_G3_100_Series.html. Plus, the wireless kit is nice for long-distance interviews and eliminates cables.
If you need a camcorder with XLR ports, I would also recommend the Canon XA20 which has a detachable handle with two XLR ports: http://www.amazon.com/Canon-8453B002-XA20-Professional-Camcorder/dp/B00C3R16O2/ref=cm_cr_pr_product_top. It's also nice and small, has built in Wi-Fi for wireless control, and records in both fast and slow motion. All of these features makes it one of the best ENG prosumer camcorders out there. Plus, it's only $2,199.
Lastly, my suggestion for a shotgun microphone would definitely have to be the RODE NTG-3. It is one of the most popular shotgun microphones in the business due to its durability and crisp sound. I have seen them on many productions and have heard great audio come from them even in bad situations. Here is the link if you want to explore it further: http://www.bhphotovideo.com/c/product/563798-REG/Rode_NTG_3_NTG_3_Precision_RF_Biased_Shotgun.html.
Hopefully that helps! Not all of these suggestion will be spot on, but hopefully it will give you an idea of where to go.