Have towed multiple Vipers 30K+ miles in enclosed trailers using R-hooks in the factory holes (as pictured above). Cross the straps front and rear and use HD ratcheting tie downs with hooks. Make sure you have a couple of "wraps" of the tow straps on the center of the ratcheting part of the tie down. Check the straps when you stop for gas or food and tighten as necessary. They really just need to be snug, so don't kill yourself making them super tight.
I've had no problems with the splitter to tie down strap clearance (and my ACR is lower than "smooth track" ride height) but you will likely have to trim a small area of the CF around the oblong hole in the frame if you have an ACR. Dodge did not think this through very well (ACR's will be trailered more than other Vipers) and as a result, partly covered the front oblong holes in the frame with a small section of the CF splitter. Trimming it is not a big deal and easily accomplished.
Call or email:
www.awdirect.com for more info on towing accessories like straps and R-hooks. Very helpful, knowledgeable company that sells to pros. Never had a car come loose in any trailer while many other Viper friends have had cars come loose. It's never pretty.
Placement of the D rings in the trailer floor is important as your tie downs won't work well if they are too close to the car front or rear. You should check the trailer you are going to borrow for D ring placement before you take off.
Would not recommend the E-track for reasons above (strength) and don't like the idea of using tires to tie the car down as I don't want to chance messing up my alignment, even if it is unlikely.
Good luck,
Dan