There should be no difference between all grain and extract if they have the same degree of fermentability, water profile, etc. You can generally rouse the yeast with no worries, but I don't know if it will help with what you're doing.
Can you give us more info on your procedures? How much yeast and what strain did you use, what was your OG, pitching temp, ambient temp, aeration procedure, how you decided you had success in the beginning, how slow it is now, etc.