You won't need the tuner in your Yaesu except for the WARC bands as mentioned earlier.
And the REALLY good news is this: You won't need a tuner AFTER the amp!!!
The tuner in your FT-990 probably can't handle much over 3:1. The pi network in the AL-811 handles that range with ease.
But, even if it doesn't, you do NOT risk damaging the amp as long as you keep plate and grid current in limites.
When you tune the pi-L network on the amplifier, you will be adjusting to achieve a specified plate current. After getting the right plate current, check the grid current. If the grid current is within limits, then you can operate the amp safely - and don't care what the SWR is. If the grid current is too high, and you have the LOAD control fully clockwise, then you can simply reduce the drive from your FT-990 to keep the amp's grid current in line. Whatever power you can get without exceeding grid current limits, is perfectly safe.
The old tube rigs were just as rugged. With tubes, you give up the convenience of no-tune, but you gain the advantage of "can't break it if you watch the meters".
Also, if you connect the ALC line between the amplifier and the FT-990 and calibrate the ALC (instructions are in the Ameritron manual), then the amplifier will automatically reduce your FT-990's drive power if grid current starts getting too high.
AM