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Keep in mind that OOTP 2006 is not yet fully designed to allow totally custom leagues using historical players.
You can import a league and players from the Lahman database, and you can actually delete entire divisions and teams, but you cannot alter the very core structure of the league, such as the division into the two sub leagues of the AL and the NL. You can rename those sub leagues, but you cannot delete one of them.
However, you can leave one of the sub leagues empty and simply generate a schedule based on the filled sub league. You'll get an error from OOTP, but I guess you can still click past it and proceed anyway.
You should also be aware that you have to create your baseball universe first and then edit the league structure through the 'other functions' menu in the league setup screen. Unfortunately, this means that the teams that you delete will show up in your league history as 'earlier teams'. It will show their names and the year that the franchise was supposedly active, which would simply be the starting year that you selected when you created the game.
If you choose to delete some teams and keep some of the others, then I assume that the history would show the deleted teams as earlier franchises and will show your renamed teams as current ones. You could also rename teams, but keep in mind that this will rename those teams for any career stats that you keep from Lahman. In other words, the franchise abbreviations will be applied retroactively to past stats. However, if you're going to clear all career stats for players, this will be a non-issue.
Also, I have discovered that my previous answer about the wildcards is not entirely correct. The only way to allow more than one wildcard team to qualify for the playoffs is if you have more than one division in your league. So, if you want four teams to qualify for the playoffs, you have to have at least two divisions. Then you can setup the league so that both division winners and two wildcards will qualify.
As a general rule, you need to keep in mind that OOTP 2006 is really lacking in the ability to create fully customized historical leagues, and it also does not allow any leagues to be added or deleted after you've created your baseball universe. You can edit league structures and that's all. And obviously this is even limited.
This has been a major area of disappointment for people who bought OOTP 2006 and expected the freedom to do the kinds of projects that you're proposing. I think that some of these issues will be addressed in OOTP 2007, but that means that everyone will have to wait until next
spring to have full power to customize their leagues the way they want.
To answer your final questions, you can simply release all the players right after you create the initial league. You can delete teams and divisions and then add teams per your preferences. Then you can schedule an initial draft. If you choose to keep some teams and delete others, I'm not sure how this will work. Maybe the players from the deleted teams will be free agents, while others will already be with their teams.
There are different algorythms for player development based on their level of minors and whether they're playing in the majors. I assume that free agents would develop different than players in the minors. If they're not playing, then I doubt that they can develop. The can probably only deteriorate.
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