Hey rwilner, welcome to the forums. Awesome story! I think it is really cool that you did this for your dad. It is one of my dreams one day to buy my dad his dream car!
As for answers to some of your questions here is what I have to offer:
Q: what is the best thread on doing the balance shaft and timing belts?
A:
Clark's Garage Home Page is a great source of technical information that many Pelican Parts members recommend. Go to the Garage Shop Manual link. This will take you to step by step instructions for changing the belts.... among many more good tutorials.
Q: - should I replace the fuel lines as a precaution? What's the best kit?
A: A fellow member (fiily) recommended this to me recently and I agree that you should definitely change them. Here is the info in the post he sent to me...
Now update your fuel lines in the engine bay for $110 here 944 Fuel Line Kit 1983 - 1989 and $93 for the fuel jumper line here 944 Fuel Jumper Line - Damper to Rail, the long $110 fuel lines get cut into the hardline behind the passenger front fender liner, and routed up as the original unit do. The jumper, just unscrews and gets reinstalled in the same place as the factory one. Make sure you relieve the pressure in the gas lines 1st.