There are no short cuts when it comes to upgrading - particularly on a heavily customized site.
IF you have followed the over-ride rules and have a well-maintained CUSTOM template, then upgrading is less of a hassle - but it is still quite detailed.
All code FILES you customized must be COMPARED with their CORE counterpart in 1.3.9c, to make sure that important code changes are incorporated into your customized files.
Also, additional MODULES may not necessarily be compatible with 1.3.9c, so you will have to look at files that such modules may have over-written, to see that they too incorporate essential code changes.



