1) You should run the front that the team is running. As a 49ers fan, I use the 3-4 and the Ravens playbook since you MUST use a 3-4 playbook when you change the depth chart to the 3-4. As far as it being as effective in reality, I think thats more on how you play. If you blitz a lot, it could work out well but you could also get burned.
2) Sorry, I dont deal with custom playbooks but im sure others here will help you out.
3) Yes, you can run the 3-4, 4-3 or both but I suggest only using one or the other, not both because teams like the Cowboys, Jets, Raiders and Vikings are 4-3 teams first with the 3-4 base defense. Bills have a few 3-4 base fronts and 4-3 base fronts but I cant remember how many off hand. Play a quick game with Bills at Bills and you can easily check it out. Also, using both the 3-4 and 4-3 conflict with each other plus affect the team's defensive and overall ratings.
4) If you mean, a 3rd down RB (like in Madden), then as far as I know the answer is no but you can sub in players on the fly on the play calling screen. You can however do player substitutions in the playbook manager if you want. For example, if I wanted to put Ahmad Brooks in the nickel or dime formations instead of either Lawson or Haralson, I can.
NOTE: You need FINN's editor in order to change team's defensive fronts (from 3-4 to 4-3 or vice versa) and must use a playbook to support the depth chart. There's only five pure 3-4 teams - Chargers, Patriots, Ravens, Steelers and Texans. Quite honestly, in reality, all these teams switching to the 3-4 is killing me as a roster maker because you have too many teams using the same playbook. If there was one last thing that FINN could crack, it would be the ability to add and subtract formations from every teams playbook. That way, offense could stay the same but the defense could be altered to just run 3-4 or 4-3 fronts. Oh well.
Hope this helps.