For the species swap AU, do you imagine the changes starting off fairly subtle, (a bunch of 104 troopers feeling ill because of the oxygen thing, sudden weight changes if they're shifting into a larger/smaller species) or does everyone just wake up one morning with obvious changes like horn stubs, pointy nails/ears etc?

It starts off subtle, yes. Enough so that no one notices until it's spread to several other battalions and Kamino alike.

It's simple symptoms that go unchecked with ease. Headaches, back and muscle pain, nausea, sudden shifts in taste (Ex: The great majority of the 501st is becoming entirely carnivorous so vegetable-based foods starts tasting off to them) and dizzy spells are the first sign that something strange is going on. The changes pick up the pace after the first initial week of infection, and then they're harder to miss because they're much more painful and distressing to go through, with things such as bone and nervous structures being the first things to be changed, followed by internal organs shifting and then the external structures.

The time frame of the transformation process is also not super linear or easy to predict, since it varies between species.

Tango Squad and any clone that becomes an insectoid species has it the luckiest pain-wise and time-wise actually... Their skin starts to harden into a solid chrysalis and they just undergo metamorphosis in a couple of days in a stasis-like state rather than slowly shifting over the course of weeks like most others. Even so, waking up completely changed into something else without being aware of the transformation process is very traumatizing, so insectoid transformations are psychologically tasking.