Thanks for the help everyone. Turns out that tools for 1-1/4 PEX are not something the smaller plumbers in my area typically have. They all recommended going back to the company that plumbed our house when it was built last year since they obviously have the tools.
The ironic part about this over-sized supply line is that my family is apparently quite frugal with our water use. I checked our usage with the water company and we have only been averaging 4,000 gal/month (33 gals/person/day not counting the baby). Our other two kids each take a both or shower every day so I expect only a slight increase as the baby gets older. We had guests twice in the last few months and our highest usage was 6,000 gallons when we had 3 extra adults and one kid staying here for almost two weeks. We go much higher in the summer (16,000 gallons!) but that's all from irrigation and won't affect a softener.
I also checked our tubs for max flow rate and the only one that's not anti-scald is putting out about 5-7 gal/min when we draw a bath. It could go higher but then it is coming out ridiculously fast and we'd never use it like that.