"Another big difference is the new job would be about a daily commute time of 1.5 hours driving compared to 36 minutes round trip on my bicycle"
I would take the job "as is" assuming I can improve the daily commute. Maybe move closer to the office, car pool, etc. Have you calculate how much is the cost for 1.5 driving (gas, maintenance, wear and tear, car insurance, your time)?
If the commute can not be improved, that is a tough decision. I would ask for higher pay, and if they say no, I am leaning toward taking it anyway because the current job seems like a dead end. One-two years down the road maybe time to get another job but at least you are on higher pay scale.