I think your A time is still too long - at 3 mos, most bubs are doing 1 hr 20 min - 1.5 hrs. And often, the first A time of the day is even shorter. Keep in mind too that A time includes eating and the wind down. I would still shorten up his A time - I think that will have a better result with his naps than doing w2s. It looks to me like the short naps are OT. I wouldn't have your A time any longer than 1.5 hrs, and it may need to be less - especially first thing in the am. Also, most bubs work best on a 12 hr day, so you do want to work towards bringing his bedtime a bit earlier.
hth
michelle