Hi themothership.
My dd is 9.5 weeks, and like you I based our day on the Baby Whisperer principles. I don't believe in leaving a tiny baby like ours to cry themselves to sleep, as I don't believe they understand. I tried the pickup put down method advocated by the baby whisperer though, and it really doesn't work with my dd - it seems to upset her more. Instead, I swaddle my dd, with her arms bent so that her hands are at the top by her chin - the idea being to stop her flailing around, but when she's relaxed she can work them out of the wrapping, as she prefers to sleep like that. I cuddle her until she is calm but even if she is still wide awake, I put her down in the cot and put my hand on her chest for a few seconds, whisper "sleepytime, dd", give her a dummy. The same routine every nap and bedtime. She sucks - sometimes for a few minutes, sometimes for much longer, then spits it out and goes to sleep. I try not to keep going in and checking on her, but I do occasionally - sometimes she goes to sleep relatively quickly, sometimes it can take half an hour or more. I figure that a rest - calm, no outside stimulation, in a quiet atmosphere - is as good as a sleep. If she wakes early and cries, or wakes in the night (she doesn't feed overnight anymore, apart from her 11pm dreamfeed), I put my hand on her chest, whisper "sleepytime, dd" and give her back the dummy, and leave the room. Overnight, if she keeps spitting the dummy out and crying, I would consider that she may have a growth spurt, then I let her feed, but try to get her to drink more the next day so she should go back to sleeping overnight. That strategy has worked so far. Do you think that would work with your little one? I think that for some babies, too much 'comforting' actually has the opposite effect, and they just need calm and quiet.
The other thing I did was to check how much daytime sleep dd actually needs, and see what pattern worked best for her. When she was younger, the 3 hour cycle was perfect, but all of a sudden dd stopped sleeping so well - for us, it was that she wasn't settling in the evening. I realised that she was still getting the same amount of sleep as she had been for weeks, but now just wasn't tired in the evening. I cut down her 1st and 3rd naptimes to a maximum of 1 hour each, and now she is back to settling at 7-7.30pm and sleeping through to 7-7.30am. She now has a nap of 1 hour max at about 9am, 2.5hours at about 12pm, and an hour at 4.30pm. The middle one is the vital one for dd - if that gets messed up, she has to sleep longer later in the day, then go to bed later. Dd currently seems not to need the full hour in the morning every day - I think she is going to drop that one fairly soon, and bring the lunchtime one forward.
I have waffled - I'm sorry. I'm just trying to offer another idea to help your dd to rest, and to reassure you that 40 minutes isn't necessarily a problem. The baby whisperer technique is good in theory, but not all babies need 3x 1.5 hour naps - 4.5 hours in a day may well be too much for a 3 month old who sleeps well at night (Gina Ford suggests 3 hours total daytime naps at that point). Maybe if she has a couple of shorter naps, she might settle for one longer nap to go with them? How long can your dd be awake happily? For my dd its about 2 hours, so she has a 3-3.25 hour cycle, followed by a 4.5 hour cycle, followed by a 3 hour cycle - don't beat yourself up if you don't go exactly with a 3 hour cycle every time. If you look at the babywhisperer website BabyWhisperer they suggest some routines for babies at different ages - the cycle could be 4 hours by 3 months, according to that (see the 'info' bits at the start of the EASY message board). If nothing else, you might be able to ask for some help from other people who use the Baby Whisperer technique.
Hope some of this helps - sorry to have waffled so much!