Not necessarily. I've converted a few bikes from the US paint schemes to the Euro paint scheme of choice over the years. No tipovers, lowslides, accidents, etc. Any every bike I keep gets the fairings removed and clearcoat applied. There is no across the board rule. Like they said pull the fairings off and inspect the frame, swingarm, subframe, and look around the case covers. If you see no damage it should be fine. You can always take it to a computrack location nearest you to check geometry.
Your temps are normal. VFR's have typically run hot, at least the versions with side mounted radiators (instead of front mount).
Since I use my '09 with the top case a majority of the time, I don't typically use the helmet lock that is on the bike. However, if you pop off the seat you'll see two metal "hooks" right about the section of where the frame starts to bend, those are the helmet hooks for the 'D' ring (see attached). If you want to get an owners manual you can go on ebay or straight to the source. Service Manuals, Owner Manuals, Wiring Diagrams, Service Bulletins - Helm Incorporated is the provider of manuals for Honda, they also have the full blown service manuals. That being said, just about everything for these bikes can be downloaded off the internet for free, but I get than having something that you can carry with the bike is preferred by most people.