From the sounds of it you are trying to put him to sleep too soon and that is probably why he is getting upset. From the time he wakes up keep him up for 1.5 hours before trying to put him to sleep. That includes feeding, changing, burping and playing. Do you give him tummy time?
For DS2 at that age even if his naps were only 20-40 mins I would just start over and put him to sleep 1.5 hrs later.
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