It's now possible to view a short manuscript of the Vilna Gaon in its entirety online. It was printed in 1882 under the name קיצור היכלות הקדושה להגרא ז"ל (מגוף כי"ק)י in יהל אור (pp. 72-74; 130-132 in the hbooks link).
I can't vouch for the total accuracy of the following statement, but according to the notes on this manuscript, today only four autograph Vilna Gaon manuscripts are known, and this is one of them.
Part of the The Braginsky Collection, called to my attention by Ishim ve-shitos.