By the way, I thought a little about Haarlem, Utrecht and Leiden... but Utrecht and Leiden are also student towns with housing problems. I don't know about Haarlem, except that family homes in good neighbourhoods are almost the same price as in Amsterdam.
As for Amsterdam: you might be able to find something affordable in the bad, unpopular neighbourhoods such as Geuzenveld, Osdorp, Bijlmer, certain parts of Noord. But they're unpopular for a reason of course.
I completely understand the fear of losing your professional tools. I'm freelance, so my entire working life is in one laptop.
I use Dropbox to back up everything on my hard-drive, and make sure my insurance (either travel insurance or local contents insurance) covers all my important stuff. So far, it's been a complete waste of money as hostels will either have lockable storage (key-cards for doors, with the codes changed for every guest, and your own padlock for any lockers).
I'm a huge fan of hostels when arriving in a new city. It is honestly one of the best sources of up-to-the-minute free information on everything: Work, vacancies, renting, sightseeing, cheap eats, et al. This especially applies to Amsterdam, which is hugely popular for 'buitenlanders' (foreigners) here on working visas.
If you're not comfortable (and I also understand being slightly apprehensive if you've not stayed in hostels before), please at least consider spending a few nights in a hostel here and there. You'll make a couple of friends, put your toe in the water with the hostel experience, and find the cheapest beer :-)
I just recommended these on another posting: airbnb.com and crashpadder.com are agencies that arrange rooms or apartments in private homes. I lucked out in April in A'dam with a double with bath, kitchen privileges and a garden {!}. Check them out; a room will obviously be cheaper than an apartment, and at 1000 euros you will find something, although your budget is marginal.
Hi
I've just stayed in A'dam with http://www.amsterdamcityapartments.com
Flat was more than decent and prices are OK. People were very helpful.