So my question deals with the radio use in the command phase.

So lets say my Boss squad only has 1 radio and I call in a long tom attack, can I still use it to issue a command to another unit more than 12 inches away.

In my option the spirit of the game would say no as its busy for the phase, but according to the RAW I can find I can still use it to relay orders to another unit .

So am I reading the rulebook correctly or did I miss something.

You're reading it right. He's just multi-tasking.

Also, when issuing FFE, the Command Squad gets a Reaction Marker. When issuing a command to another unit, they (the Command Squad) do not. So it makes sense in spirit of the rule terms as well - the command to another unit is a short burst transaction, "go here. Shoot there." type of deal. FFE is a process of walking the arty on target - "Fire one, wait, adjust 50 long, 20 right, FFE!" kind of thing.