Salvete!
We undertook a stocktake earlier this year using Koha 3.4. We didn't use the stocktake module though. What we did was return all items through the circulation desk. This changes their last seen date to the current date. Once we had done that I then made a report which showed the biblio/item details and included whether the item was on loan or not and the date last seen.
Any item not on issue or not seen prior to the date the stocktake began was considered missing and its status was changed to lost.
We have undertaken stocktakes using the same process and with three different Library Management Systems and have come to the conclusion it is the best method. Using a laptop with scanner and wifi connection means you aren't dragging books to the issue desk.
Below is the report I use, which could also be used as a shelf check list. If you only have one branch then take out the highlighted line. Not sure that it would work in your version but worth a try :)
I concur that this is a stellar way to ensure accuracy. A side benefit is that you can shelf read, weed, and shift as you go along. Cheers, Brooke