In the Install, Available Software dialog go to the Available Software Sites... and make sure that everything other than Indigo repos disabled.
You can almost certainly advance quite some way, but very recent versions run into trouble with needing Java 8 for which really old versions of Eclipse don't work. I suspect you could advance to Xtext 2.8.
If you require your legacy work to be useable by anyone else you should agree on the version of Xtext that you use. Xtext 2.0 thru 2.3 improved quite a bit, without being totally faithful wrt API. 2.3 thru 2.6 are more interchangeable. IIRC 2.7 has a breaking change as does 2.9.
I would recommend 2.3.1 if you really need to use an old version.
Indigo has some overt incompatbilities with Java 8 and probably many obscure ones.
It seems very strange that your legacy requirements allow you to use Java 8, which did not exist for Indigo, yet require you to use Indigo which is embarrassingly old.
If you really really want to use Indigo, get a consistent Indigo environment going then selectively install more recent functionality that you may find helpful. As I noted earlier, Xtext 2.8 may be as far as you can go.
I am working on a massive tool that is Xtext based and till this day it was only 32 bit. We work on a 32 bit Indigo eclipse with Xtext 2.9.2 installed, so that's what I am trying to do but on a 64 bit eclipse to provide a 64 bit version of our application. To migrate to another version of eclipse it would take a lot of time and would delay us for a lot time.
If you have a working reference just make sure that all the 64 bit installs are for very similar versions.
Replicating a legacy environment may save you time today, but in the long term attempting to live in the past costs an ever increasing amount of time. If you are motivated to change one aspect then you are setting up a new environment so you might as well make it a sensible one. Using a perverse mismatch may work if you are lucky, you have demonstrated that it doesn't, so don't waste yet more time on a blind alley that you will surely abandon fairly soon.