We came through Pakistan in September and had to apply for India Visas in Islamabad as Omie suggests. You're only option as far as i know. It took 5 working days (no express option as i recall) so effectively it takes a week and cost us 40 euros each for a 2 or 3 month visa. Getting into the diplomatic zone in Islamabad is bit of a hassle, best get a cab and get there in the morning, as they close the visa section at 1pm and it can take up to an hour or so to get through the 'departure lounge' for a compulsory bus round the zone. It was all very straight forward so not to worry.
The idea of spending a week in islamabad (although there a couple of great places to eat) probably isn't ideal but....
Hope that helps. Just so you know once you've got the visa, you are allowed on the toll road to Lahore as long as your bike is over 500cc, despite people telling you that you need a permit. Just rock up, tell them the engine size and on you go. It's twice as quick as the GT road but you'll be so desperate to get down to Lahore you won't mind!