Focus-Recompose - it's showing you the focus point you used to lock focus, wherever that point ends up in the final composition. The camera doesn't know which direction or how far you moved after locking focus. If you lock focus and recompose, you're moving the focus-lock point location away from the subject you focused on, and that's how it shows up in the image. FYI, the technique works ok for 'slow' lenses, but with fast primes shot wide open it results in a backfocused shot, due to the geometry (in fact, it does at narrow apertures, too, but the DoF is deep enough to mask the focus error). Side note - have you considered back-button AF? It's a handy technique that lets you control focus independent of the shutter button.
Screen protector - I don't bother. The outer glass surface is scratch resistant and easily replaced (by the user, with a part from Canon). A screen protector also adds glare, to which the bare screen is pretty resistant.
Neck Strap - skip it. Get a Blackrapid strap that puts the weight on your shoulder, much more comfortable.
Camera bag - a Lowepro Toploader Pro 65 AW would also work. I have one, love it, also have the Pro 75 AW for longer lenses (100-400, 70-200 II, etc). The 65 AW holds the 24-105, 16-35 II, etc., up to the 100L Macro IS. With the Lowepro, you can use their other products with SlipLock attachments to attach to the side of the 65 AW - a Lens Case for a second lens, QuickFlex pouch for a Speedlite flash, etc.
CPL - possibly. The B+W Käsemann line has no color tint (many CPLs do), and is robustly sealed. I have many B+W filters (UV on almost all lenses, Käsemann CPLs in 77mm and 82mm, 3-stop and 10-stop NDs in multiple sizes), all are excellent.
Hope that helps...