Some babies need more support with pu.pd and extending naps, and it sounds like he's one of them.
Is Olivia and Will in the same room? What about for the time being, since Olivia seems to be improving with her naps, moving her into a different room.. recreating the sleep environment-- dark room, if you can move her cot, same bed linens. What may be happening is they are responding to each other during pu.pd.. making it harder for Will to settle down.
This will give you more time/energy to settle Will back into sleep. Generally, when a baby wakes up at the 45 min mark screaming, it's overtiredness and inability to return to sleep.
So 1. make sure he is falling asleep independently
2. Get support with Olivia while you work with Will. Friend, family member? It's just for a short time.. if she's almost past it, then it won't be for long. If not, start your plan on a Friday, get help for that day, and then you have the weekend for hubby to help you out.
3. When he wakes at the 45 min. mark, give him a chance to resettle to sleep.. and then go into pu.pd mode. I'm not saying to CIO, just give him an opportunity to resettle. When you go in, be as discreet as humanly possible.. you don't want him to hear or see you enter the room.. some moms have gone into the room around the 30 min. mark, done a wake-to-sleep method to disrupt the cycle. And then gone into pu.pd. OR just go into the room at the 30 min mark, give him a chance to stir and an opportunity to resettle, and then go into pu.pd if needed. The key is for him not to know you're there..
It sounds like he's a spirited fella.. spirited babies benefit from a darkened sleep environment, since visual stimulation can actually keep them awake and make it hard for them to settle into sleep.
Another thing.. prior to putting Will down for sleep, prior to his wind down routine, give him a pre-wind down. Some spirited babies benefit from a very calm, low key activity prior to their wind down.. like a carry walk around the house or slow dancing. This helps him body to release the calming hormones, to help him settle into sleep.. whereas an high energy activity prior to wind down may set off the cortisol hormones, which actually keep infants awake and brings on short naps.
Hope this helps!