I do not have a TS2000 but I have a TS480SAT
You must have the data rate set  correct on both ends and a kenwood mode 
selected on the 998
Also the ts2000 side must be in external amp mode
Also you MUST have the second cable rca plug from the ts2000 to the 998 and 
then from the 998 to the amp ptt
the data cable between the ts2000 and the 998 is NOT enough

Thanks
73 Neil Sablatzky  K8IT
Allstar Node 41838 KITLINK
Allstar Node 42087 KITLINK HUB
IRLP Node exp0068
Echolink K8IT-L
WIRES-X K8IT 11479 Room 21479

--------------------------------------------------
From: "Richard B. McDonald" <[log in to unmask]>
Sent: Saturday, January 16, 2016 11:14 AM
To: <[log in to unmask]>
Subject: Re: Ameritron ALS-1306 Not Going into Bypass Mode During Tuning

> Hi Neil!
>
> Thanks *so* much for your below!  This is really helpful.  Please let me 
> ask
> you to tell me exactly 1) what the three menu settings are for the TS-2000
> and 2) what the two settings are for the 998.  I may not have these 
> correct.
>
>
> 73,
> Richard KK6MRH
>
> -----Original Message-----
> From: For blind ham radio operators [mailto:[log in to unmask]]
> On Behalf Of Neil k8it
> Sent: Friday, January 15, 2016 4:53 PM
> To: [log in to unmask]
> Subject: Re: Ameritron ALS-1306 Not Going into Bypass Mode During Tuning
>
> Make sure that the ptt output of the ts-2000 goes to the mfj-998 amp input
> jack then the mfj-998 amp output jack goes to the als-1306 ptt input this 
> is
> the only configuration that will work
>
> Also make sure that both the 998 and ts2000 are enabled for external tuner
> control with a kenwood radio, and both are in external amp control mode
>
> This is three menu settings in the ts2000 and two in the 998 tuner
>
>
> to troubleshoot
> put a wattmeter on the output of the ts2000 and ensure it drops the output
> power to 10 watts while tune button is pressed
>
> if that works verify that the tuner tunes the antenna before power is
> restored to 100watts do all this with amp turned off
>
> then reset ts2000 output power to 30 watts and verify amp gets keyed only 
> in
> operate mode not standbye mode
>
>
> Thanks
> 73 Neil Sablatzky  K8IT
> Allstar Node 41838 KITLINK
> Allstar Node 42087 KITLINK HUB
> IRLP Node exp0068
> Echolink K8IT-L
> WIRES-X K8IT 11479 Room 21479
>
> --------------------------------------------------
> From: "Richard B. McDonald" <[log in to unmask]>
> Sent: Friday, January 15, 2016 6:46 PM
> To: <[log in to unmask]>
> Subject: Ameritron ALS-1306 Not Going into Bypass Mode During Tuning
>
>> Hi!
>>
>>
>>
>> With my Kenwood TS-2000, I use both an Ameritron ALS-1306 amp and an
>> MFJ-998
>> antenna tuner.  Both the 1306 and the 998 are connected to the TS-2000
>> with
>> their respective interface cables.  I also have the 998's "Amp Enable
>> In/OUT" RCA cables connected to the 1306.
>>
>>
>>
>> However, when I press the "Tune" (AT) button on the TS-2000, the 1306 
>> does
>> not go into bypass mode during the tuning process.  I cannot figure out
>> why
>> this is happening : (  I would appreciate any insights anyone has on 
>> this.
>>
>>
>>
>> 73,
>>
>> Richard KK6MRH
>>
>