When the loops are bypassed, are the SEND and RETURN outputs left floating or grounded?

When the loop is bypassed, the SEND loop is left floating and the RETURN loop is connected to ground with a 220r resistor to minimise noise.

Can I control Amplifier Switching with the ML5?

No, the ML5 is not designed to do that.

Does the ML5 have stereo loops?

The loops on the ML5 are all mono.

My ML5 mutes when switching.

This is part of the Muted Switching feature to remove the occurrence of pops for certain pedals (usually pedals using a voltage charge pump). The feature can be toggled ON or OFF by holding down Switch D before powering up.

Can I use the ML5 to switch effects in front of the amp as well as in the amp FX loop?

Yes, it is possible. There are 5 loops on the ML5, so assuming you wire it like this:

Guitar --> ML5 IN
ML5 Loop 1 Send  --> Front loaded FX 1 In
Front loaded FX 1 Out --> ML5 Loop 1 Return
ML5 Loop 2 Send  --> Front loaded FX 2 In
Front loaded FX 2 Out --> ML5 Loop 2 Return
ML5 Loop 3 Send  --> Amp In
Amp FX Loop Send --> ML5 Loop 3 Return
ML5 Loop 4 Send  --> FX Loop pedal 1 In
FX Loop pedal 1 Out --> ML5 Loop 4 Return
ML5 Loop 5 Send  --> FX Loop pedal 2 In
FX Loop pedal 2 Out --> ML5 Loop 5 Return
ML5 Out --> Amp FX Loop Return

It will work.