I've been doing the same thing. Often enough that it was doing my head in a bit, which is why I've come on here after almost a decade (I think). Essentially I, like others, thought the album was disjointed and needed some punching-up sonically in points. The key thing I did was take BTW off the front where it feels wasted, especially as Daydreaming is a huge tempo shift. There are only two sets of tracks joined aurally: 3-4 and 10-11. I thought a bunch of songs could work as an opener but after playing around a bit I decided on The Numbers, and then I wasted time and even some money thinking 'OMG - 'the numbers' - they're saying that once we have the tracks in the right order it will make a phone number and we can call and find out Nigel's favourite ice cream! Alas I couldn't crack it. I'll just hold off on buying him ice cream. For now. +82 is Korea by the way...
8 - The Numbers - the song which feels like a sampling of so many of their sounds over the years, so appropriate as the lead-in I felt, due to the fact we will get a few familiar elements to come on the LP. And the opening of it feels like the unbottling of an album with people tuning up (even a hint of 2+2=5 with the zapping sound a bit like the plugging in guitars...). For these reasons I think it also feels like too much of a re-start to be in the middle of the album
2 - Daydreaming - I know a lot of people say it's too early, but it really pulls you into the world of the album immediately. No messing about. And the opening of it feels like 'finding the groove' on a record
5 - Ful Stop - Pick up the momentum after Daydreaming
7 - Identikit - Great track so we can still rock
9 - Present Tense - This is where I hit my main area of doubt. I really like Identikit into Present Tense, and his singing about the way he dances fits well after Indentikit, given it rocks and it's after the 'broken hearts, make it rain' line which can be seen as a bit of a cynical lyrics (the 'we make money from depressing music' criticism... which of course I don't believe is true, but Thom's lyricism often goes for those layered meanings).
But I know PT works so well in the back 3 too, and I've had it there after GE and it's great. But I still can't shake that Idetikit into Decks Dark is too disjointed. I've tried Spectre here, but it doesn't really fit... BTW from memory worked well, but then I wanted to put GE after it and 3-4 was pushed too far to the back. I've tried putting 10 and 11 after PT here, in that same TKOL way of having a feeling of two EPs back-to-back, but it's such an album stopper due to all the silence after TLW... So on balance I think PT lives here and then we go into the album centre-piece:
3 - Decks Dark - feels like 'coming up for air' with the tinkling pianos, but the atmosphere once it kicks off suggests we are deep in it - so I like this as a centre-piece instead of track 3. I sort of think of this album as being a moon-shaped pool to dive into, and this is the centre of the pool, so we're the longest from getting over the emotions of it - 'in your darkest hour' - but there's a coming up for breath despite being down deep... A moon-shaped pool would be a sphere, after all, so if you get to the bottom you could take a breath.
4 - Desert Island Disk - it is mixed aurally with Decks Dark so 'must' go here, although Glass Eyes kind of works in between them too, I feel it's a bit of a weak, meandering track, but sometimes it really suits my mood and again works as the centre of the album as it is the calm in the middle of the storm, and Thom is seeing a way out of it, 'across a street, to another life, catching my reflection...' (also as an aside, the 'you know what i mean' bit reminds me of the Nirvana track 'You Know You're Right' and maybe this is a reflection of the anger he felt mid-break-up, where the desire was to rock out to heavier music)
1 - Burn The Witch - picks things right back up after the double slower track. It has such an abrupt start that it only fits in certain places and this is one of those. Also the chugging strings sort of has some of that anger which wasn't reflected sonically in the last song, but seemed to be there in the lyrics. And that energy feels needed for the lyrics to come in Glass Eyes next...
6 - Glass Eyes - The lyrics fit the end of the album, after the emotions of a break-up that have been present in previous tracks. Annoyingly in my mixing the tracks around a lot, I also often want to hear BTW immediately after it too...
10 - TTSSRMPMBMT - Another track which feels like a bit of a re-set with the way it opens, but overall is very much an album closer in my head.
11 - TLW - so much silence at the end and it is connected to track 10 aurally so it pretty much has to be here. I kinda feel like it's a bit tacked on. Sorry, as I know a lot of people are saying they love it. I look at it as this is a 'break up' album of sorts and Thom has put this song in perhaps because it was written for Rachel originally and it just felt right to get a bit of the sad irony of it here. All that emotion now spent.
Spectre?* I like the idea of fitting it in as it is sooo good, but I've only just done it and my version of it isn't as crisp as the AMSP tracks around it (they're all downloads from Radiohead so maybe it was mixed differently - the info on the track has it as 'Joint Stereo' while AMSP is 'low complexity' VBR. Certainly it would help add weight to the back of the album as DID, GE, and TLW I think need some help around them. I can see it coming after GE or TTSSRMPMBMT or just on the end as a little bonus before we cycle back around to The Numbers
Now of course the problem is I'm used to hearing this order, and after taking a break from the album for a month or two and coming back to it, I started playing around again thinking it wasn't quite there, but I've settled back onto the above. I'd love to get some feedback from people. One thing with the name 'A Moon Shaped Pool' is that it implies randomness. If, say, Stanley just left 2 or 3 different paints pooled outside for the moon to shift around creating the mix we see on the front cover (I'm guessing this may be the idea) then maybe the idea of using Alphabetical Order is similarly that this is kind of a 'natural' way for outside forces to shape the album. So there isn't a 'correct' order. Or the clunkyness of the 'natural' way is just how life is. But I prefer to think of it as songs to dive into and I enjoyed the album way more after moving songs around. Maybe you feel I should have been more patient will the alpha-order?