Well before Tom Doak (and not counting MacKenzie's early moving of #17 green, or the loss of the fairway tree at #16)....
-- Holes #2 (originally 510 yds) and #10 (originally 495 yds) were converted from par 5s to par 4s, I believe to avoid crossing entry road.
-- #6 shortened when original tee (located to right of #5 green) was removed.
-- At #9, the present green was built in the 30’s (possibly by MacKenzie), though for a time this version and the original existed side-by-side.
-- At #10 and #12, barrancas fronting the putting surfaces were filled in/minimized.
-- At #15, some wild bunkering within the fronting barranca was largely grassed over.
-- Some MASSIVE tree growth.
-- A fair number of original bunkers are missing throughout, though having examined pre-War aerials, I can categorically refute the claim (made in Margaret Koch's The Pasatiempo Story) that "During the 1940s, approximately 100 bunkers were removed to facilitate play time."
Cornish & Whitten list Robert Muir Graves, Gary Roger Baird, R.T. Jones Jr. and Clark Glasson (no middle name?) as having made changes but when I inquired a few years back, the club could not confirm the presence of all four.
I'm quite certain that Tom Doak has made a positive difference, but Pasatiempo does not play precisely as Dr. MacKenzie designed it....
DW