As a 49ers fan myself, I definitely understand how you feel and know what you're trying to do. The best advice that I can give you is to use the Ravens playbook since it has the 3-4 defense in it and of course is the same that Nolan used when he was in Baltimore.
I personally keep all the teams the way they are in the game because you cant change the depth chart so while you can use a 3-4 playbook, your team's depth chart will still be what its originally programmed to be.
I simply use my 49ers as is and just switch some players around. For example, I had OLB Manny Lawson as a DE last season which is somewhat realistice because he played DE in the 4-3 at NC State and would do so in SF if we ever run a 4-3. For this season though, im going to play him at his normal position at OLB because he's a starter and Ulbrich isnt.
My 49ers defense currently looks like this -
DE - Young*, Douglas*, McDonald (R), Oliver, Haralson
DT - Franklin*, Sopoaga*, Rayburn, Fields, Cohen (R)
OLB - Lawson*, Moore*, Banta-Cain, Green, Moore (R), Bockwoldt
MLB - Willis (R)*, Smith, Ulbrich
CB - Clements*, Spencer*, Harris, Strickland, Hudson, Goldson (R), Brown (R)
SS - M. Lewis*, K. Lewis
FS - Roman*, Vaughn
* = starter
Of course, it's up to you. I just keep all the teams the way they are in the game. I wish that I could edit the team's name, stadium and logo but I cant and because I cant, im stuck with them as they are. It's minor though so its all good.