Waite himself made clear on two occasions that he "spoon-fed" PCS with only some of the Major Arcana. The Court Cards generally follow the Golden Dawn ones found among Westcott's papers (possibly drawn by Moina Mathers). Obviously, he gave Pixie direction on all the Majors. I feel he left much of the specific imagery in the Minors up to Pixie, with some exceptions.
Swords and Pentacles are the most specifically Masonic suits with Swords being the Hiram Abif story (3rd Degree Masonry) and Pentacles following his outline of the role of the Initiate that he gives in Encyclopedia of Freemasonry. Three illustrations from the the Hiram Abif ritual carry elements that appear in the cards. Wands and Cups are more Grail, with Cups being the most literal illustration of a story: the Joseph of Arimathea story in The Metrical Romance of Robert de Borron (as Waite retold it in his book on The Holy Grail, published the same year as the deck). The 2006 Llewellyn's Tarot Reader was a much earlier report on my research and has been superceded by new findings.
It's also pretty obvious that Waite gave Pixie texts to work from - she was trained as a book illustrator (that is: how to illustrate a text). It's clear that with the time constraints, she drew very much from her own store of imagery, adapting visual elements from other of her works and from her surroundings.
Marcus and Tali have uncovered previously unknown sources for some of her images, some of which are very convincing and some which deserves consideration only in light of the truly convincing evidence.