Chapter 28 of the Rabbit 6000 Users Manual describes the Input Capture capabilities.
Unfortunately, there isn't a lot of sample code for using the Input Capture feature of the chips. You might be able to use Samples/Rabbit4000/ic_test.c as a starting point.
You'll need to configure TAT12R, TAT8R and TAECR to make your timings off of the raw peripheral clock. And GCSR for the peripheral clock to use the main oscillator (which I believe is only 25MHz).
I'm not sure of the details, but with 25MHz=40ns, there's some wiggle room there. I'd make use of that sample, trying to configure a low divisor. Then send in a known pulse length and see what your reading is (the count should * 40ns should be close, or a power-of-2 fraction of the actual length).
You'll need to write an ISR to store the counter value somewhere that your main program can retrieve and process it later. Hopefully you're measuring a short pulse with long quiet times so you're only seeing thousands of pulses a second and not millions.