How are you sitting with your bassoon? As Topher said, the bassoon should cross your body with the bell to the left of your head. Bring the seat strap to the edge of your seat, and bring your bassoon across your body. Another possibility is the position of your left hand. You might be doing something called a "claw," (an old teacher's word from his college professor) where your left hand is covering the tone holes at an angle instead of coming straight across the instrument. This causes tension as well as forcing the weight of the instrument to be put on your left hand. Look at your hand position compared to that of some professionals you can find on youtube. Playing bassoon should not be physically painful, if it is, you are doing something wrong.

The whisper lock is a convenience, not a necessity. to accomplish slurs with these notes, air will help you. From a low Bb/B/C to an F, a whisper lock is not necessary, especially in fast passages. Support the notes with adequate air so they speak clearly.

E natural would be fixed by clipping just a 1/2 mm or so of the tip of the reed. Which is almost impossible without a tip clipper, a reed knife and block can get about 1mm off, but for such a small amount such as 1/2mm, a tip clipper is much more precise. If you do not know how to do this, I would recommend either asking some that does or not doing it at all. A trick for the sagging E is to hold down your 3rd finger on your right hand while playing an E. DO NOT get used to this fingering, it is not standard, it will just raise the pitch closer to being in tune. It is useful for rehearsals/performances when you needs to get the E in tune and it's just sagging left and right. Reed adjustments are tricky, don't attempt unless it is with your teacher. You could end up killing an otherwise good reed. Buy a few, break them in, rotate them, let them dry before putting them away or by a case with little vents on it so the reeds don't mold.