i know you have said that H needs that early bedtime but i honestly think its that thats the problem!
He had a good pm sleep yesterday,i think you could have stretched that bedtime out more.
3.10-6.40 is only a 3.5 A,thats way to short IMO,thats something a young baby is doing.i think you need to push that bedtime A time,he should be able to do at least 4.5 on that good nap.i know you said he needs a low A to bed so if thats the case you need to do it slowly but i think you will find thats the prob.
if it was me id just push for 1 nap,2 naps always gave us an EW the next day so it could be that not helping too.if you really want to stick to 2 naps id do what he was used to but push that bedtime.i know towards the end of the 2-1 a lot of mums are having to have a later bedtime to get 2 naps in but H is having 2 naps and an early bedtime that most mums would do for a 1 nap day. Do you see what im saying?