Sounds like a good plan - An Alaska cage and a 12" Silent runner
As you've just changed the substrate, I would wait another week or so before moving him, till he's settled again.
You mentioned a couple of things - fall risks and reaching water bottle. Both are solved by having deep substrate, and it's one of the best things you can give a hammy is lots and lots of deep substrate - as you mentioned he can burrow in it. Also a house that is open underneath on top of the substrate is a good idea so they can bury hoards under the house and burrow down and be snug. Plus makes it doesn't sweat inside like a house on a plastic shelf eg.
If you don't have a house then a shoebox makes a good house. Cut the bottom out and a hole in the long side for a door and keep the lid as a lift off roof. Then you can check inside without having to take the house out and his nest falling apart.
With the substrate, you can go up to about 1cm below the top of the cage base without it falling out of the bars and also heap it up in the middle where it can't fall out of the bars. It will cushion any falls and you won't need to clean the cage as often. It will use a lot of substrate the first time you fill it, but after that you can mostly spot clean taking a handful or two of soiled substrate out now and then and replacing it with a clean handful and mixing it in. I used to do that and only needed to do a "big" clean about every 2 to 3 months, so in the long run you save on substrate and avoid stressing out your hammy (they get stressed by too much cleaning, or cleaning everything at the same time as it removes their natural scent).
I would also suggest getting a litter tray and some Chinchilla bathing sand. Hammies will usually use a litter tray - then you only need to empty the litter tray once every 5 days or so and the rest of the cage stays dry (unless you have a hammy who pees in the wheel! Some do). You put the litter tray in the spot the hammy has chosen as his pee/toilet place, with the chinchilla bathing sand in. If you put it anywhere else they won't use it
They choose where the toilet is going to be! Usually not far from the house and in a corner. If the house is big enough, they sometimes use a corner in the house, so another reason a shoebox house is good as it's big enough to fit a litter tray inside in one corner, if that's what happens.
I have this one - it's a good size for a Syrian, easy for them to get in and out of and easy to clean.
https://www.amazon.co.uk/d/Houses-Ha...=Hamster+potty
This is the Chinchilla bathing sand most people use. I find it lasts quite a while but usually get two at once to save on the postage. Viovet sell it as well. Or you can click on other sellers on Amazon if you don't want it as an add-on item,
https://www.amazon.co.uk/Supreme-Pet...a+bathing+sand
If you are getting the Silent Runner, I really think it's worth spending the extra £5.50 for the cage mounting plates - especially for the Alaska. With the mounting plates you screw the wheel to the bars rather than use the stand. It means you can have it as high as it will go in the cage with just a very small clearance gap above it. This means a) The hamster can't fall on the wheel or try and climb over it. b) The higher the wheel is the more substrate you can have underneath it and the more useable floor area there is in the cage.
Cage Attachment for Silent Runner
It's the best and sturdiest cage mounted wheel there is, in my opinion. And still silent.
I would suggest setting up the Alaska, fill the base with substrate, fix the wheel and put a couple of toys in there, and maybe a familiar toy from the old cage as well, and let him go in it for a play and explore, maybe 2 days before you plan to move him over. He might get a bit freaked out and want to come out again. So then leave it another day and do the same again. The second time it will be more familiar and he should explore it more and spend some time in it (all depends on the hamster how they react - ours was nervous and it took two exploring sessions
. The day after that, pop him somewhere safe like a pet carrier and take all the substrate from his old cage and sprinkle it on top of the new substrate in the Alaska - doesn't matter if it's a bit high by then, you can compress it down and pile it up in the middle.
Move the rest of his things across (or the ones you want to keep) and try and put the toys, water bottle and food bowl in a similar location/layout to before. Put the new house in (partly under the shelf might be a good place, or in the empty corner at the from opposite the wheel).
Don't be tempted to clean things before moving them over - just move them over as they are - they will be fine for a couple of weeks. You could also put some of his old nest inside the house, and also put lots of new nesting material in a pile somewhere in the cage near the house, so he can take it to rebuild his nest. Torn up strips of plain white toilet paper are safest for nesting, and they like it.
Putting a bendy bridge over the house door can tempt them to nest in it too as it makes it nice and dark inside, plus the bendy bridge makes a ramp up to the flat roof top.
Maybe scatter some food on the substrate as well as in the food bowl and hide a couple of treats on the substrate in different places, before popping finally moving him in and that should distract him from feeling nervous.
Once he's moved in, it's like going back to basics when they first come home. Leave him alone for 2 or 3 days to scent mark and settle in - unless he shows signs of wanting to come out and play. Then don't clean or move anything for two weeks. If it does get a bit whiffy in the odd area, then just spot clean a handful after the first week.
Adding the odd new thing is ok after the first week or two, but don't move things around or take things out or it'll stress him.
Hope it all goes well!