It does not sound correct, but I’m not sure what you mean. Instead:

Les modifications que tu m’avais dit de faire ont été faites.

If you were asked to do modifications, and they were done.

Les modifications que tu m’avais dit faire ont été faites.

If that person told you they would do the modifications, and they were done.

Nope sorry !

If you question the agreement of past participle dites :

Les modifications que tu m’avais dites […]

que is object to the verb dites, therefore it should agree with it (feminine plural).

But here :

Les modifications que tu m’avais dit de faire […]

que is object to the verb faire, therefore dit shouldn’t agree (it has its own object, which is de faire).

Les modifications que tu m’as dit faire

The meaning is different as explained by Pierre. No agreement for the same reason as above. This phrasing doesn’t sound very idiomatic to me (western France), maybe ‘Les modifications que tu dis avoir faites’ will be prefered.

Note that dit de faire ends up sounding like dite faire in speech, I can imagine this could cause some confusion in a non-native speaker 🙂