Before starting - do you have any backup of the other league at all? You might not need to cut the whole thing, there may be an auto-save you can use?
Presuming that is not the case or you just want to make lemonade and start over, I'll look at your questions individually.
First, the league totals. What I have done that works pretty well is to collate various eras' totals for each of the stats sought in the LTMs and then divide by the number of seasons totalled. Or, even better, have it reset to a fixed rate like 100000 AB.
This will give you an average figure to use.
So if you wanted to cut out the deadball and PED ERAs to give you some sort of cross-sectional total to use, go 1925 to 1994. BBRef should allow you to group them and give you the totals or you can do it in a spreadsheet. Then just divide by 70 and that is your yearly total.
Enter that into the LTMs on the day before OD and check the Lock Totals and Auto-Calc boxes. This will be the total used every year.
The big challenge with this is getting the BABIP right - just go to
THIS link and, again, select all of the seasons you want to include and it should give you an average. This being unweighted means it'll be off a bit but it should work OK.
You might want to do a few different ones and switch them in and out as you see fit to mix things up. While the AI engine provides some variance, it may not be enough for your tastes. You play it your way.
With regard to strategies and the like, just figure out what settings you want to apply. Turn off the auto-adjust option in the STATS & AI tab. Enter the settings.
Sadly, this area can be a bit tricky, although having the locked stats can actually tend to help here. On OD, the game will try and change the strategy settings and also the non-stat-related league totals (EG sac bunts, steal attempts). So just keep a record of the settings handy and cross check it after you have reached Opening Day.
One key here is to never underestimate how closely all of these different settings work together. So plan it out properly and get the stats / LTMs and settings aligned as much as possible in a logical sense if you want good results. For example, don't have STEALING BASES set to RARELY then STOLEN BASE ATTEMPTS set to a contradictorily high figure.
Trust me, the more thought you put into all of this at the beginning, the more you'll get out.
(and, though I'm sure I need not tell you this now, BACK UP YOUR DAMN SAVES, BOY!)
Let me know if this helps, or if you need more info.
Good luck.
G