I believe most have addressed some of the timing concerns with various things, and given the current world state of affairs and the great unknown of the next year to come you may not even have this trip planned still? But since I did a lot of what you are planning as part of my trip to Wales last summer, one thing I wanted to touch upon is the Thursday day trip. I did something vaguely similar last year on my Saturday - staying overnight in Porthmadog I drove, starting around 9 am, to Criccieth, visited Criccieth Castle, drove to the Llyn Penninsula to Morfa Nefryn, walked to Ty Coch via the beach, had lunch, walked back to the parking lot via the golf course, drove to Portmeirion, spent 1.5 hours there, drove to Harlech Castle, spent about an hour there, and then drove to Nanteos Mansion outside of Aberystwyth. Was it doable? Sure - I did it. Was it wise? I DEFINITELY wish I had more time. I have to say it only took me about 25 minutes to walk down the beach for MN parking to Ty Coch and same vice versa via the golf course. But I wish I had more time to see more of the Llyn Peninsula - so many cool secluded beaches and coastal areas.
For Portmeirion, I feel like I saw most of it in the 1.5 hours I was there - but what I was sad was that I didn't get to linger. The whole thing was taken in at a brisk clip. I would have liked to have a meal down by the water, really slow walk thru the nooks and crannies. I've never seen the Prisoner, but I suppose if you have seen it you may want to slow the pace down to identify things from the show.
I did take the Welsh Highlands railway from Porthmadog to Caernarfon on a different day - doing the lunch time train and having lunch onboard. I also did the Snowdon Mountain Railway on yet a different day as well, which was fun - but as mentioned departs from the foot of the mountain in Llanberis. The Porthmadog train took about two hours to Caernarfon and then I took a bus back to Porthmadog to give me time for site seeing in Caernarfon (excluding the castle which I did the same day as the Snowdon Railway trip). I also took the Snowdon Rail at lunch time - I believe a 130 pm steam train, which is about 1 hour up, 30 minutes at the summit where I grabbed a snack, and 1 hour back down. Parking was a bit tricky and you have to plan well if you are there on a busy day. The village of Llanberis is pretty, there is another train across Llyn Padarn, and a castle (Dolbadarn?) there on the Lake as well that are worth checking out.