You are looking at catching up with YEARS of deferred maintenance in most cases. However, one you baseline the vehicle you should be able to have a reliable daily driver. The auto trans has a bad reputation, it is a very good transmission. Most people ignore them and as a result have had little to no service. If you need to replace or rebuild it you are looking at big$. Now a FJ62 with a 5 speed conversion would be a sweet daily driver, but again you are looking at big bucks to convert it to stick.
Dynosoar