Were we to know in advance that we would win, say, n seats in a region, then it would be straightforward to use STV to select n candidates from the potential candidates and put them in the top n places in our list. If we don't know n in advance (which we don't!) then we can perform this operation for every possible n, i.e. from 1 up to the number of seats available in the region, and attempt to construct a list whose top n candidates are those victorious in the nth selection ballot. (There is really only 1 ballot - the division into n ballots is notional.)
This ideal solution fails when a candidate elected for one value of n is not elected for a larger n. In such cases either the STV result for a smaller n must constrain that for the larger (top-down) or vice versa (bottom up). Reasoning that the Green Party would be unlikely to win large numbers of seats in any region, we opted for top-down.
If a count is proceeding identically to an earlier count, and an exclusion by lot is required, then the result of the earlier lot should be taken as read. Otherwise the lot must be recast. (cf 5.6.3)
5.3.3 and 5.4.2 For the purpose of these rules (i.e. receiving transfers), a candidate elected in a previous count (not stage) should be treated as a continuing candidate for purpose of receiving transfers during the count, until they are deemed elected again.
Where regional parties have agreed to adopt gender balance constraints, then the usual constraint rules shall be used. This usually means excluding all the candidates of a particular sex at the beginning of an even-numbered count.
Each region was free to determine its own gender balance formula. For example one region might require a list of half men and half women with no constraints on position, and another region might require that the top two candidates were a man and a woman with no constraints on the other candidates. Whatever formula was chosen, this was applied within the system by excluding any ineligible candidates at the beginning of a round. Hence the top place on each list would be open to both sexes, and subsequent places would only be constrained in the event of an imbalance. Notably the London region decided not to impose a gender balance formula, and the top three candidates are all women.
On each ballot form there is a notional candidate called "Re-Open Nominations" (who is of indeterminate sex). If Re-Open Nominations is elected to the list, then there must be a fresh election for that place and lower places on the list. This is a distortion of STV which could be used by a majority to deny minority representation, although there is no evidence of this happening. STV, rightly in my view, omits this sort of negative voting, but it is popular in the real world outside public elections, such as in student unions.