failing to read data pin based on clock pin with setWatch and digitalRead

The issue you're hitting is that setWatch timestamps the events and put them in a queue to execute with JS - but as you notice it's won't execute JavaScript in the interrupt itself.

One way around this is to actually watch the data pin for changes as well:

var currentDat = 0;
setWatch(function (e) { currentDat = e.state; }, dat, {repeat:true});
setWatch(function () {
        if (i < 52) {
          a.push(currentDat);
          i++;
        }...

However reading clocked data is a really common thing to want to do, so in version 1v96 I added the ability to also record a separate data source using setWatch:

setWatch(function (e) {
        if (i < 52) {
          a.push(e.data);
          i++;
        }
}, clk, {
    edge: "rising",
    debounce: 0,
    repeat: true,
   data : dat
});

So that should do exactly what you want.

More info at: http://www.espruino.com/Reference#l__global_setWatch

As @Wilberforce says, depending on what you're trying to connect to there might also be a way to set up the underlying hardware to help you out.