Propulsion
1) The instruction manual says " use pieces of foam rubber to hold the (fuel) tank in place".
Use foam rubber under and on the sides of the tank. The tank should not be jammed in so tightly that it can't move at all, but the foam should provide vibration cushioning.

2) The "vent" tube goes to the muffler for back pressure, the "Fuel Pickup" tube goes the the carb.....What does the "Fuel fill" line plug into? This isn't explained in either the boomerang manual or the engine manual.
With the engine out in the open, and the carb fully accessible, you can use the fuel supply line for fueling. Simply pull it off the carb, fill the tank, and replace it. The third line is not necessary.

3) The engine wasn't exactly a perfect fit onto the engine mount....Is this normal?
Looks straight enough to me. Adjust it until it's as centered as possible in the mount. I do see your fuel lines are much too long. Shorten them so they make short, gentle curves, with no binding and no excess slack.
Linkages

1) The connection to the servo's is my main concern.
Those are EZ Connectors. Easy for the beginner to use, but I, personally, don't like them. The brass cylinder should rotate freely, but not wobble. BE SURE to tighten the set screw well!!!

2) The manual has a section on control throws. It's just a list of up and down numbers. How do I set control throws? Does this really matter?
Yes it matters. The amount of control throw governs how your plane flys. I'd set the elevator with about 20-25 degrees of movement each way, and the ailerons about 25-30 degrees. This angle is measured at the control surface. A protractor is good for this. The rudder should have all the movement you can get, and the nose wheel should only move about 1/4" each way.

Now you see why I seldom recommend an ARF. The plane often needs modifications, and many times, as you've found out, the instructions are marginal, at best, for a beginner.

Make sure all the control surface hinges are glued in well. Tug on each one. The fuel tank klunk should be about 3/8" away from the back wall for proper fuel draw.

Keep asking questions, we'll get you through it.

Dr.1