I'd say do a search on the 6Ps and go though all that stuff first. you will find that good PM will solve a lot of issues. make sure all connectors are good and clean of corrosion and have the correct clips. also it worth investing in a conzult connector (cheap enough on ebay) and getting conzult, ECUtalk and dr330zx all free software and will help to diagnose issues.
and sorry but I don't know about doing the egr with box off.