1. You can get this 2nd skin bandage that goes on top of blisters to keep them from being so painful. Works pretty good, I forget what it's called, something like beaver skin or gopher skin...
2. You need to stretch and warm up properly prior to any CV activity. If you haven't developed a sweat on your brow during your warm up than your not warm enough.
3. Probably patello femoral syndrome, this could be due to not going down far enough on your squats causing your muscles to develope unevenly and pull on your knee caps. Check my post in the link below.
http://forum.bodybuilding.com/showthread.php?t=4743593
4. Don't lock out, never lock out on any exercise.
5. Are they turning cramps like charlie horses? Eat more bananas and stretch before bed.
6. Good question but if you think it's dehydration than try hydrating better before working out. Remember, by the time your thirsty your already dehydrated.
Not falling apart, it's just part of the game. If you feel you need to take a break than do it or you can try changing your routine a bit to give your body a break.
Good luck