Can you use the mc5jr with the fm3? If so, how does one connect it for switching scenes?

Yes you can. Just connect MC-5jr with a normal midi cable (5-pin) to the Midi in of the FM3.
On the FM3 set Scene Select to CC34. You can find this parameter under Setup - Midi/Remote - Other
 
Voes also makes an "M-box" to do this but it really makes sense more for power and processor in a rack.
Indeed.

I don't think it is compatible with the MC5jr though.

The MC5-jr is compatible with the M-Box.

To be clear, the MC5-jr (and also the MX series) have a 7-pin Midi connector.
This will work perfectly with a normal 5-pin Midi cable.
The additional pins (6 & 7) are used to get power from the M-Box with a 7-pin Midi cable. this device will split the signal in Midi Out, Midi In and Power

In case of the Axe-Fx Standard, Ultra, II you can skip the M-Box and connect a 7-pin Midi cable directly between Axe-Fx I/II and MC/MX device. In that case, power adapter is connected directly to the Axe-Fx I/II.
 
Just for clarity: for use with an fm3 I'll need a separate power supply and a five pins midi cable ? Howbeit as the fm3 is a floor unit...no use to feed over 7 pin cable...
 
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