To quote from the "Memoir", Tom made "short notes on passages of Scripture and points of doctrine.....as early as 1816 and were carried on to 1860."
The date 1816 is of interest to us because it indicates that some of Jane's novels had been published and he might have read them. Especially for us, is that "Persuasion" was published shortly thereafter wherein we find Anne's conversation with Captain Benwick in the last 4 paragraphs of Chapter 11 which you can read here:
In that place we find these words of particular interest: ... she ventured to recommend a larger allowance of prose in his daily study; and on being requested to particularize, mentioned such works of our best moralists, such collections of the finest letters, such memoirs of characters of worth and suffering, as occurred to her at the moment as calculated to rouse and fortify the mind by the highest precepts, and the strongest examples of moral and religious endurances.
Following that train of thought, we find in the Memoir Tom refers to these: Archbishop Leighton's works, Robert Daly, the Bishop of Cashel, and Lord Mandeville. All these need to be researched.
Next item, Jane died in 1817 and due to their family connections, Tom may have heard of Jane's illness and passing which led to some reflection about their discussions and/or her books.
Which leads us next to those family connections. Off the top of my head, there was an Austen who married into the Lefroy line, so I will assume that the family 'news' traveled back and forth. Another item to be included in the research.
Now, will someone please step forward and volunteer to use all this material to make a Jane/Tom connection? That should keep you busy for awhile.