string content = File.ReadAllText("data.txt");
var replacements = new[] { "A", "B", "A" };
int index = 0;
string result = Regex.Replace(content, @"[a-zA-Z]+",
m => replacements.Length > index ?
replacements[index++] : m.Value);
This will execute MatchEvaluator
for each found word, and replace it with value from appropriate position in replacements
array.