I'm not 100% sure I understand the situation. And I don't have a straightforward answer.
First, read my documentation if you haven't already. The comments on "Leitner/Short Term Goal" are short though, most is on Spaced Repetition (SRS), though you should know a little about my SRS and know the differences.
http://orangeorapple.com/Flashcards/AboutSR.aspxThere's not many settings for Leitner. If you want to reduce the penalty for a wrong answer, change "Reduce Streak (on wrong)". If you want to lengthen the time after re-seeing a missed card, increase the "Max cards in Round".
I think my Leitner works well for smaller sets of cards, e.g. 50 to 100 cards max. One possible issue with a 1000 card deck is that let's say you are starting fresh, and you get a card correct (maybe on first time, or maybe you just got it wrong and got it correct on the retest in the next batch of 30), you won't see that card again until you've gone through the entire deck of 1000 cards and got all of them correct. Maybe that's what you want as it lets you see all cards in the shortest time frame, but the disadvantage might be that you don't get those periodic repeats quick enough to start getting them learned. In your case, as you've already been studying, it should already have statistics
So the simple answer is, turn on Leitner, adjust those two settings if desired, and let it do its thing. When you start a "set", you'll get an intro screen telling you how many cards remaining in set. For example, you might get 300, meaning the app things those 300 cards are ready to be studied again. After going through those, next set of cards you'll get missed cards (wrong, then correct) plus a new set of cards you last got correct.
If you want more consistency between the review times on an individual cards, you can consider using SRS. Each cards will have an interval, which is ideally the amount of time you are just about going to forget the card, and the card will then become "due" at that time. You'll see cards you don't know well more often generally, but then you won't get to new cards as quickly since you are focusing more on lower interval cards, until you get those intervals up. If interested in this approach, you can let me know and provide more suggestions.