The shuttle is the biggest expense hands down, but 100% worth it, especially if you use a good shuttle company. The less vehicles you end up shuttling, the less expensive the trip.
This is where the big 'gas guzzling' SUV's that folks love to rip on come in very handy.
Two years ago seven of us ran the Main in early June, shuttled one vehicle, spent 3 days on the river (higher, faster water that time of year) and ended up paying $125 per person for everything - permits, shuttle, food, gas (from SLC, UT - there and back again), etc. We ran with one cat, one raft, one duckie, and four hardshells.
The Main is a fantastic trip, well worth doing. Enjoy!