Yes, the
USB version of the high-flow flow meter has an internal temperature sensor. It's not really mentioned anywhere but it's ideal for measuring the coolant temp without adding a bunch of wires and fittings - assuming you're fitting one anyway, that is.
The alarm option is an rpm header. You can configure it to send an rpm signal (static value I think, rather than the flow rate) to a motherboard header with the idea that if the alarm goes off it stops sending an rpm signal and the motherboard does something useful with that. Depends on the motherboard, some have the option of beeping at you if a fan stops (all but useless, the Aquaero will do this already) but some have the option of powering off. It is also possible to configure the alarm header as a closing switch so you can use Aqua Computer product number
53217 to piggy-back it onto the motherboard's powerswitch header so it effectively holds the power button down forcing a power off.
The splitty has a jumper to switch it between splitting fans (speed wire attached only to one header) or splitting aquabus (all wires connected to all headers) - see
manual. If you have a spare splitty to dedicate to Aquabus, you can plug one cable from its input to the Aquaero's Aquabus High and then cables from the splitty outputs to all your other Aquabus devices. Note the 5 amp max load on a splitty if using lots of fans.
Since the Farbwerk has two Aquabus ports (both high) you can use it to chain connections but you don't have to - depends if it makes your wiring easier. You can go Aquaero to Farbwerk then to splitty and then to flow meters but if you can find (or make) a 4-pin splitter, you can do it without using a splitty: Aquaero to Farbwerk, 2-way splitter to each of the flow meters. Key thing with a y-cable is it needs to be 4-pin (if you want to run power over it so you don't need to also run USB) and it needs all wires to connect to both ports. You specifically don't want the cable like that for fans but some come that way anyway - doesn't look like any of the ones OCUK carry do for 4-pin splitters.
If you add a PowerAdjust it also has two Aquabus headers but only three pin so you could add it in the chain but not last before something requiring power. You could go Aquaero > PowerAdjust > Farbwerk (adds power back in) > splitter > flow meters.
The idea would be to run something like this as suits your loop:
fan1: pump
fan2: case fans
fan3: rad1's fans (via splitty)
fan4: rad2's fans (via splitty)
PowerAdjust: rad3's fans (via splitty)
Your pump seems to be a 4-pin fan header and a SATA power. If you're into crimping your own fan pins on, you could (once tested and happy it works) cut the sata power off, crimp fan pins on and put them into the fan plug since the Aquaero can safely supply enough power to run the pump. Will work fine without doing this but makes it neater wiring wise since you have one less wire to run.