Help!

1. The calorie counters on gym machines aren't particular accurate. I wouldn't use them as a judge of much of anything. In fact, I'd can the elliptical machine altogether - why not just swim/bike/run?

2. You only bike once a week for 35 minutes? Of course, you're getting tired on the bike. Biking seems to be the hardest to make noticeable gains in, and requires A LOT more time, even years to get really good. More miles are needed, not necessarily more leg strengthening work - though, as a caveat, strength training is a VERY highly debated topic here, so you might want to go to the strength training sub-forum here for more information. Biking is one sport where you can train well past the mileage you'll need to race - go for some longer distance rides - weekends are good for this.

3. Sounds like you are wearing yourself out - you shouldn't be sore every day, as puellasolis said. x2 with her suggestion of finding a training plan, whether that's developing one of your own with Triathlete's Training Bible , or an easier option, the plans available here on BT -  most include a rest day. If you're still building up endurance and strength, you need a day to let your body recover from the new stuff you are doing to it. If your muscles don't get a chance to heal, they can't rebuild themelves and become stronger. And from what I've been told, I would be careful of "sprint work" with running - tons and tons of threads on here will tell you that intervals/speed training really shouldn't be done by newbies. (FWIW, I've seen an increase in my speed in simply running consistently - only been running for a little over a year.) Could be contributing to your soreness and could also lead to injury. Along the lines of soreness, make sure you STRETCH after your workouts - esp. after running. That will help you recover more quickly.

I am not an expert, but this is all stock-answer information that I have gleaned from the last year and a half of tri-training and the wonderful, knowledgeable folks on BT.