My husband and I are traveling to St. Petersburg this summer and the route we chose was to more or less go on our own.
We are working through a travel agency , Nota Bene Travel, and they've been very helpful. Through them we arranged hotel accommodations, they are helping us with our visas and picking us up/dropping us off at the airport. They'll also arrange private tours with a car and an interpreter. The rates for this service are really reasonable. I'm not sure we'll use them all the time, especially for in-town tours like the Hermitage, but we will using them for out-of-town excursions.
Here's the link:http://nb.travel.spb.ru/
On the site it looks like they only arrange tours packages, but given the experience I've had with them it looks like they're pretty flexible. They've been very responsive, e.g. they always get back to me within 24 hours.
Good luck on your travel plans, Reed.