Multiple peripherals using SPI with a Mega
What's so special about pin 53

Pin 53 is the slave select pin of the SPI peripheral. As such it has a bearing on how the SPI peripheral operates.
It is intimately tied to the master/slave operation in that when it's an input SPI works in slave mode, and when it's an output it runs in master mode.
So to use SPI in master mode, whether you use pin 53 or not, it must be in OUTPUT for SPI to work at all.
There is nothing much wrong with your methodology, but one thing is missing: the initial state of the chip select pins.
You should always start with all chip select pins disabled (i.e., HIGH) rather than in an unknown (probably low - I'd have to check the datasheet) state - the exception might be pin 53 which SPI might itself set HIGH for you.
So if you add:
digitalWrite(FSYNCA, HIGH);
digitalWrite(FSYNCB, HIGH);

right after setting the pinMode for your pins and still use both pins 53 and 49 then it should work.