The alignment I had to do was very minimal and only on a couple tracks out of 10 song recordings (with 8 tracks on each).  The output from the Fostex VF160 was only stereo analog so only two tracks could be transferred at a time (using my two channel recording interface unit).
 
Maybe I was just lucky but it worked OK.

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I'm with Chuck on this one your very best bet is to look into a 4 channel interface. Then the process will be very straight forward. 
But that said, the next best choice is what you already though of and record in one pass but to two machines. 
It would work for shorter songs for sure. I've synced up tracks from 2 digital recordings in the past and around 3 minutes they are fine.  So what you could do is start and stop the Yamaha at places between songs. 
 
What you'll want is a very obvious transient to line them up. If there isn't one on the recording, you can always add one if there is room between songs without danger of erasing wanted material. Just record a slap to a mike on Ch 1 and 3
Funny the Yamaha MT100 was my first serious home studio. Used to sync midi using channel 4. 
 
But A new interface would be my first chioce as this is always a welcom addition to any studio. 
At the bottom price points here's 3 good ones
The Focusrite 6i6    https://www.sweetwater.com/store/detail/Scarlet6i6G2
Tascam us4x4    https://www.sweetwater.com/store/detail/US4X4
Pre Sonus 6/8  https://www.sweetwater.com/store/detail/Studio68
 
 

Thanks to all who responded here. I've now got plenty to think about although a new Focusrite is on the cards.