Jim,
Okay...I just assumed that you had a normal "keying" line (make/break) from the Flex to the amp?
And, that the Mercury AT tuner also had a "keying" input?
So, that you'd simply put the tuner "in between" the amp and Flex, in terms of the key line of course (not the RF coax feed)
But, I guess the Mercury AT tuner does not have such keying line out?
So, does the Mercury amp have a "key line interrupt"? (where the Mercury amp accepts an "interrupt" signal from the Mercury At tuner?
Also, all "12vdc" Icom HF rigs made in ~ 30 years have this ability to send a 10 watt tune carrier, usually from a front panel "TUNE" button....so, have a look see of the Mercury manuals (amp and tuner) and see if they mention the Icom "TUNE" function?
You never know?
That's the extent of my generic thoughts...
Hope it is of some help? If not, just send an email to Kenny in Miami, and he'll get back to you, I'm sure. (that's the advantage of buying a Mercury, rather than MFJ, or for that matter a SPE, Flex, etc....from what I hear, Kenny actually cares about his customers!)
73,
John, KA4WJA