I'll be a taker. Manual J can work on an old home, I have one. But you have to know your home, the wall construction, and air leakage, jsut like any home. Just like on new homes, construction quality varier widely. I have a 87 year old home that dispells all myths about old homes being leaky and poorly insulated. It's performance rivals many highly insulated new construction homes with all sorts of fancy modern materials.
A good contractor knows the homes and what construction is common in the area. A homeowner also has some responsibility to know soemthing abotu how his home is constructed, or he'll end up wiht a poorly designed system. If in doubt, existing utility bills can provide some useful information. IF you only have a $150 natural gas bill in Jan, you won;t need more than an 80k furnace. Then by evaluating the amount of shade and windows you have, and what climate your in, you can determine what AC size will match that furnace size to a certain extent.
It is a science not some magic. It's seems like an art form because some vairales are not always easy to determine. Thermal mass (usually a lot higher in older homes) is not taken account in Manual J.