So I went back at calculated all 16 games you posted for your 49ers chise.
Your team avg plays per gm (including sacks taken)
63.3
The CPU
49.8
Total
113 per gm
You may want to increase your qtr. by 1min.
Do you use acc clock by chance?
Also the pace at which you pick plays matters, if you use coaching suggestions vs picking through plays.
I've recently gone back to picking my own plays b/c coaching suggestions are so limited.
So I also need to up my qtrs by 1min more than likely
Keep in mind, your 49ers have a rock solid D, when healthy and your running game w/ your Oline and AP are just too much for other teams to slow down.
You did when the T.O.P battle in almost every game with that team.
I know it's much different when your using a less skilled Defensive, and offensive rushing team.