The Quarry Bends section is very different now, having been altered (in the 80s?). Brandish was a sharp 2nd gear corner until quite recently and the changes there would definitely trimmed a few second off he lap. Windy Corner was another that changed significantly.
Bedstead, Hillberry, Signpost, Creg and the Nook / Governers sections have been improved though with probably less impact on lap-times. The Sulby and Cronk-y-Voddy  starights are also much smoother now.