I restored an FTDX560 a couple of years ago. As I recall the BFO crystals are HC-6/U types which are relatively widely available, although a newer holder size should be OK in the relatively non-critical and low-ish drive circuit. There are several suppliers left who make custom crystals if you can't find a used device. Send them a copy of the oscillator schematic when you order.
One caution re used and original crystals: the crystals in the Yaesu were spectacularly awful in terms of frequency aging and activity level. Fortunately, most could be tweaked back into tolerance in my transceiver but the difference between the FTDX-560 and a Collins 32S-3 from the same era was stark. Before you get too far into the repair you might also want to have a look at the crystal filter. By carefully setting up the BFO frequencies I was able to get pretty good USB and LSB audio on transmit and receive but I gave up on the idea of trying to obtain a CW filter - there weren't enough variables left to juggle!
Be gentle on the sweep tubes when you fit them, and make sure you read the manual regarding tuning the PA. You need to be quick and accurate. My radio managed a genuine 300W CW/PEP output on new tubes but, if you value your ham neighbours, don't run it at anything like that SSB level. About 120 W PEP out gives just OK IMD but at 300 W you're in the IM3 ~ -20 dBc territory which is, in fact, about consistent with the original spec of -25 dB with respect to PEP.
I also replaced the hardest working electrolytic capacitors (including the can types) and quite a number of tubes (including the 7360 balanced modulator). With careful alignment the radio turned out well and was something of a nostalgia blast, my late 70s first "real" radio having been an FTDX401B.
There were many modifications throughout the series to try and correct Yaesu's weird mic amplifier design but often the easiest way is just to use a high output (or amplified) mic and roar at it. Better mods move the mic gain pot to the right place and fix the negative feedback fraction.
73, Peter.