Have you done a dyno run to get real-time data for analysis? Gen 1 FJR's have a number of characteristics that contribute to fueling inconsistences. A re-flash, PC or Dobeck will not solve but kind of cover up to degree. Validate what the problems are first. Complete a compression, leak-down, and fuel pressure test with a dyno run before you introduce changes to the current system causing yet more problems to solve.