My first word of advice is to start the game after each patch to make sure it was applied correctly. The version number will appear on the splash screen.
It will be a long process to get the game up to speed, so be prepared. Setting up the mods can be longer. Be sure to keep a vanilla backup of the game in case you mess anything up so you don't have to start from scratch.
As for joysticks: I use a Thrustmaster T.16000. It has great bang for buck ($40 retail) with a hall sensor, twist for rudder, and a throttle slider. In my experience, the similar Saitek Av8r went bonkers within a year.
I kept my stick on the right, and the mouse on the left. It takes a few days to get used to, but it makes flying and looking around very easy. However, I recently bought a TrackIR, which makes looking around very fun. If you're handy, you can use freetrack or facetracknoIR.
Il-2 1946 is the game we all play here. Il-2 Birds of Prey is the console version, and Il-2 Wings of Prey is the PC version of the console game (very odd, I know). Il-2 1946 is based on an engine from 2001, so the graphics aren't cutting edge anymore, but it's arguably more fun than BoP or WoP.
1946:
WoP:
