1. If your QR affects the spin of your hub, you need to adjust your cones properly. Also, I'd reccomend a Shimano or Campy QR to ensure that it doesn't slip.
2. If you're finding it difficult to line things up, a bolted axle can make things easier as you can tighten the drive side to get the chain tension right, then do the left to get the wheel position right.
3. Big tires and fenders don't always play nice. You can fit wider fenders if your frame will allow, adjust the fender position, or go with narrower tires. Or, if everything fits once it's in, you can deflate the tire, install the wheel, and then inflate the tire again.
4. Surly sells free/free hubs in 135mm. You may be able to swap the axle to fit your frame or cold-set your frame to fit the hub.