Is it possible to extend setWatch to include timer interrupts?

Do you have a link to obtain a copy of the assembler?

You best bet is to upload it, then hit up-arrow to see a copy of what was uploaded. Eg.

var adder = E.asm("int(int)",
"movs    r1, #3",
"adds    r0, r0, r1", // add two 32 bit values
"bx  lr"); // return

Gives var adder = E.nativeCall(1, "int(int)", atob("AyFAGHBH"))

and you can just use atob("AyFAGHBH"):

var data = atob("AyFAGHBH");
var addr = process.memory().stackEndAddress-data.length;
poke8(addr, data);

What is the opcode for disable and enable interrupt?

You don't actually have to disable interrupts - I believe the ARM does this for you (the only thing that will interrupt you is an interrupt of higher priority, which you should probably allow anyway).

Does the ARM use a special return from interrupt? If so what is the opcode?

It's just a simple bx lr I believe (a normal return) - the ARM instruction set is quite nice :)

How to queue the Javascript?

I don't think that is possible for now...

You'd have to toggle the state of a pin, feed it back, and then use setWatch. There's info on toggling pins states under the ACCESSING IO heading on the assembler page