I feel so loved!
That's part of the reason I like EASY is because sleeping doesn't come directly after eating.
If most of his naps are under an hour, then he's definitely OT by the end of the day, thus the problem with the last nap. So let's see if we can work on that....
Does he use a pacifier? Or does he have a lovey (a little animal or something to hold)? At 12 weeks, I think we were starting to wean from swaddling with my dd - have you ever swaddled? Abby sucks her thumb and has a lovey (Pink Bear) and we no longer swaddle. Tracy has a wind down she calls "The 4 S ritual" which is what we used - set the stage, swaddle, sit, shh/pat. What we would do is go in to her room, diaper change, (swaddle when we were doing it) close blinds, say "night night outside", sit in the rocking chair and talk a bit about naptime, sing a song, then shh/pat on our shoulder (we don't do this anymore), then when she's really drowsy, put her in the crib.
So cuddle time with your ds is a great part of a wind down, but he may need a bit more. I'd start the wind down at least 15 min before you want him to be asleep. So at about 1 hr 15 probably. With shh/pat, we'd start on our shoulder, then we'd keep doing it while we walked to her crib, lay her down on her side a bit, so I could reach her back, then keep shh/patting until she went to sleep. We had to shhhhhh pretty loudly, because she would often start to cry. But she would eventually calm down. In the beginning, we'd sometimes shh/pat for 30 min or more. If she wasn't asleep after 40, we'd take a break. Gradually, the shh/pat time got less and less, and eventually we stopped, because she learned how to put herself to sleep. Some moms find that rubbing works better than patting. Also, if she was really crying, we'd lean way over in the crib to be super close to her, to make sure she could hear the shhhhhh. Does that help?
early bedtdime - yep, I think if he goes to bed earlier he will not wake earlier. He's really tired. 12 hrs is about all he can handle in a day right now. It will also likely help with his naps.
Also the 3-4 mos time is a massive time of transition, so that makes sleeping a bit of a challenge. He may be getting ready to move towards a 3.5 hr EASY, and then at 4 mos, probably a 4 hr EASY, so it's a whole lot of routine tweaking at this stage of the game. So hang in there. It does get better. I'd say try moving him more towards the routine (or something similar) that I posted and let's see what that does to his naps.