Hi there. How old is your lo?
Going from motion sleep (swing, stroller, etc) to stationary sleep is a big transition. But it really is better for him. Good for you for making the change.
Sounds like you've already gotten him to go down in his crib (GREAT WORK) and sleep for 45 minutes, so the crib sleeping may not be the cause of the short naps. It could be A times, developmental, or a combo.
If you want to post your routine we can take a look...