Rest is the most important part of working out. Its what heals the muscles and helps them grow stronger. Are you early on? It sounds like you may be pushing your workouts to more extreme then your body is used to?
You don't mention how long you have been working out? What your minimums are.. etc.
Everything you have described.. sounds like you need rest. Try alternating like traditional body building to give broad areas of muscles rest.
Is a good split to help you get as much rest as possible..
Dropdowns, also known as negative reps also cause the most "damage" might wanna rest abit more after those.
Oh ya.. eat.. eat lots.. protein to help you heal. Really you have to play with your food to figure out what helps you. Personally Paleo suits me well, my body absorbs proteins nicely and I tend not to work well with carbs in my system leaving my lethargic in the afternoon. I have traditionally done the 30x30x30 system which has suited me as well. As long as I keep my carbs lowish and low glycemic I heal well and grow strong.
Split your workouts
Grow stronger and enjoy
(throw in some other routines too.. pistol squat, russian pushups, burpees and other ploymetric style workouts)
Oh ya, TRX rocks. Truly kickass stuff. I love suspended workouts.
I do try to workout often, but I travel frequently so sometimes bodyweight exercises are all I have. Gets difficult for motivation since I truly love to move heavy things. Hopefully some of those sites help you out.
Oh.. one thing I love about bodyweight exercises are the freedom.. go play on a playground.. screw pullups, just climb arond like a monkey, don't try to touch the ground. Make challenges for yourself like when you were a kid. Betcha its still a workout