Welcome Andy,
1. The holes in the back of the stock (and many aftermarket) header pipes are factory threaded bungs that should have a threaded plug installed. There is one behind each header pipe. If you are missing one, possibly remove the other to match. Don't re-thread the hole you'll possibly want it later as retrofit oxygen sensors continue to shrink amazingly small. Its possible a local dealer will have a spare from a customer who had them install new pipes. If you plan to swap pipes, plug it with anything! Also, you can ask any prior owner if he has the header plugs.
2. What year is your bike? Its possible the stock clutch spring still resides in your bike, or its possible someone upgraded to an SR2 which is heavier. Nothing less than the stock clutch spring will do. In fact it needs to be heavier to handle the full torque.
3. There are a couple of torque settings in the service manual that are incorrect. With an aluminum motor its very advisable to follow the manual's torque settings otherwise. But for those that have been verified incorrect, look in the DOWNLOADS section (to the right of HOME) then click on the 'Reference Materials' folder, then look for a file called 'Notes from My Service Manual' it contains the torque corrections discovered and verified by several other members. NOTE: some torque specs are so small, like 17FtLbs, its uncommon to have a wrench to read that small, in which case you can get a wrench or use your experience factor. As you know, stripping aluminum threads in a motorcycle often results in loads of pain and vanishing chrome money.
Here's a direct link (but take time to see what files live in that folder they are handy as heck).
http://rswarrior.com/files/folders/reference/entry1012204.aspx
Follow the service manual's recommendation notes for when to use Loctite 243 Blue (removable without heat).