nishtdayngesheft
It is quite well known that in Lita before the war (including Vilna) almost everyone wore tefillin on chol hamoed. your mistake is in assuming that people followed minhagei hagra in Lita. In fact, even in Vilna, they did not follow this minhag or many others(except in the Gra’s kloiz). Only in Eretz Yisrael did the talmididei HaGra begin to implement his shittos. R Moshe has a tshuva (I believe it’s in the back of R Eiders sefer on hilchos niddah) where he has complaints against those who follow minhagei HaGra lekulah in Eretz Yisrael and says they never dared to do such a thing in Vilna (he is talking about zmanim there, I’m just using it to point out that the minhagei HaGra were not kept in Vilna).