There is only one version of the String Quartet, which Bruckner completed on 7 August 1862. On 15 August 1862, Bruckner completed a second Rondo movement, which has the same key, metre, and formal structure as the the first Rondo movement. The second Rondo can, therefore, be regarded as an alternative to the first Rondo.
The composition score (Mus.Hs. 19482) was first completed in 1879; it was subsequently revised sometime during the years 1880-1883. The revisions included a 20-measure cut in the first movement (mm. 245-264 of the 1879 version) and a 20-measure cut in the Scherzo (mm. 63-82 of the 1879 version). A copy score (Mus.Hs. 37289) was made after this first round of revisions.
This copy score, with subsequent alterations, was used as the Stichvorlage for the first printing of 1884. The revisions introduced in the 1884 version include a reversal of the order of the inner movements (the revised form being Scherzo and Trio followed by slow movement), alterations in the second subject of the Finale, and numerous instructions regarding tempi. Some of the revisions of 1884 are in Bruckner's hand, while others are not. The 1884 version was published again in 1945, edited by Max Alberti.
None of the alterations made in the copy score (and included in the 1884 version) were entered into the composition score. However, the composition score was revised by Bruckner sometime after the 1884 printing. (For now I assume c.1890.) The revisions included some changes at the end of the Finale.
Nowak's edition is a mixture of the 1884 version and the final version. It includes some of the revisions made in the copy score along with all of the revisions made in the composition score. Of those revisions made in the copy score, Nowak chose to include only those in Bruckner's hand. The other revisions were assumed to be inauthentic, but this is not necessarily a correct assumption. (See, for example, Symphony No. 7.)
The earlier Wöss edition also mixed the 1884 and final versions of the score. More precise details are not yet known.
At the suggestion of Josef Hellmesberger, Bruckner composed an Intermezzo late in 1879 to replace the original Scherzo. The end of the manuscript has the designation "Trio", indicating that the Intermezzo was to be followed by the original Trio and then recapitulated. The Intermezzo was published first in 1913 and then by Nowak. (Neither Alberti nor Nowak name the editor of the 1913 edition.) For subsequent versions of the Quintet, Bruckner reverted back to the original Scherzo.