Ruatha's SE4 Companion has a plugin designed to update all of your races to Gold compatibility. Unfortunately, it has a few bugs that muck up some of the files, such as AI_Fleets.txt... I forget all of the things it does, but I can dig up the post if anyone is interested. With Ruatha off in military training, a fix for his program is quite a ways off.
You can isolate which shipsets have errors in their AI files by moving all races save 20 from your Pictures\Races folder to a temporary folder, then starting a new game. You should always choose the same race for yourself, one that you know works fine.
Most of what such a program needs to do is outlined in CapnQ's guide to converting AIs to Gold compatibility, since most errors are related to downloading a shipset with pre-Gold AI.
*link* This is simply inserting missing lines where they need to be in 3 or 4 files. The rest of what needs to be done is testing that all of the lines that should be in the files are present and inserting missing lines, as well as making sure that you do not declare 5 items and only define 3.
Edit:
Actually... a few changes need to be made in AI_Design_Creation.txt. In one of the early patches, several abilities were changed in name to make them less confusing, primarily related to combat to hit modifiers. There are a couple of shipsets on PBW that have not been updated and still contain AI designed with whatever the old values were. These are listed in SE4's History.txt file somewhere, as well as in that post about Ruatha's companion program... guess I need to dig it up afterall.
edit2:
Also, AI Design Creation needs more work done on it. These abilities need to be updated from:
Combat To Hit Dec
Combat To Hit Add (and Combat Sensors)
To
Combat To Hit Defense Plus
Combat To Hit Offense Plus
Also:
Phased-Shield Generation
to
Phased Shield Generation
These were changed in an early pre-gold Patch of SE4.