I am assuming that the photo showing the bolt handle is the "before" version, made prior to cutting the stock to allow the bolt to fully close. I don't see how the rifle could have been fired in the condition shown in the photo, since the bolt lugs would not be fully engaged and the striker would not fall all the way.

Considering the number of alterations already done, I don't think you should hesitate to make others which would make the rifle more useable, including relieving the stock until there is no contact between it and the bolt. The receiver may need to be relieved also. This can best be determined by removing tha barreled acttion from the stock and determining if the bolt turns through the entire 90 degrees when locking. If it fails to do so, some judicious filing or work with a Dremel tool is called for.

This should improve the accuracy as well.