3.5 month old fighting sleep. Experienced mothers please!?

Okay. My 3.5 month old son has good days/weeks, then bad days/weeks. For instance, this past saturday and sunday were wonderful. He napped without fighting us much and slept for a solid 6 hours at night. Yesterday, he took naps with moderate fussiness, but slept horribly at night. My husband I were taking turns every few hours. Today, however, he has been fighting his naps like crazy! He is sooo exhausted. He'll scream and cry, rub his eyes, start to fall asleep a bit, then get another wind and start it all over again. The only way I got him to sleep this time was to feed for a few minutes. He fell asleep at the and then i, probably stupidly, replaced it with a pacifier and put him down. He used to put himself to sleep pretty well. We would wait until he was drowsy and put him in his crib. Now we almost always have to put him to sleep elsewhere, then sneak him into bed. I know this isnt healthy for our family in the long run. We want to set up good habits, but we are desperate. Any tips?