DS and DD both went from 3 half days preschool to full time K. Preschool was MWF 8:30-11:30 for both. DS had the option to stay until 12:30 and DD had the option to stay until 2:00. We did that for both kids one day a week. It was an easy transition for DD but a little harder for DS. He was definitely tired by afternoon and we had to up his bedtime by 30 minutes. He did well at school though and was adjusted to the new schedule after the first 4-6 weeks. I think 3 half days was fine.
I know kids who have, but most kids I know w/ a SAH either do 4-5 half days or 3-5 full days. We are doing 4 days of 9-1.
Do any of those schools that are 9-12 offer a lunch bunch or extended/late day? I don't like that 2nd option.
While I preferred the slightly longer day & 4 days a week, she was also off all summer and had 3 months of nothing aside from swim lessons, etc. So, who knows. I think it was good practice.
Public kindergarten here is 5 days but for the first few months it goes till about 12:30 and then it extends to 2 to get kids used to the longer day.
Not sure if DS will go to public or private K yet but next year he will be in preschool 4 days a week (wed off) from 9 to 12:15. He will also do summer session that year before at the preschool so kindergarten is a huge shock after a long summer break.
Edit: I would stick with the morning option even if it's a day less. If he's napping then the afternoons will be a mess for him and you. And I'm guessing kindergarten starts in the am so that would be more of a typical schedule to get used to? Like the whole morning routine of going to school etc. By the time kindergarten rolls around the nap will probably be gone and he will be older and able to deal with being away from home longer so I don't think you have much to worry about!
Honestly I think it is fine to 3 days if that is what most people do. My kid went to all day care (with prek in the AM). The kid who sits next to her didn't go to anything. He's rocking the academics and had a bit of struggle with separating from his parents. My kid separated beautifully but has struggled with the academics of K. By mid year most of this is all sorted out.
ETA: There is no naps in our K. I think the kids got like 10 mins of down time in the first month but that was pretty much it. Most days the last period is choice time (aka play time) or a special (music,art,computers) so they hard work of the day is done by 1:30.