Run Training - Painful!

I sit on the trainer for 3 hours and sweat my ass off and walk away feeling great with no aches and pains. I run one hill a couple times and can't walk for two days - what's up with that?! I'm finding there's a distinct difference between running on flat, smooth surface vs. running off-road, up-hill, off-camber, and over rocks/roots/obstacles. It's obvious I really need to be doing this training to prep for the Tough Mudder in May. Ricky Brown wants to go to the Tohickon Creek on March 20 (Ralph Stover State park) to watch the kayakers on the dam release weekend (it's too cold or he'd probably do it) and I'm anxious to go along 'cause the Ralph Stover Park will be an excellent place to train. The woods are nice and open and we can easily go off-trail and down to the river and the banks are s.t.e.e.p -- just what the doctor is ordering for the Tough Mudder. Depending how things progress, I may sign up for a 10K in Danville on April 17. It's flat (rail trail), but it'll be a good high heart rate workout for a longer distance run. (yes, I know, 10K really isn't long -- but it is for me!). This is a nice change and I'm enjoying the switch up to a run focus for a spell.