I've got the same ongoing status with my GT500, and I also ordered the Shaker 1,000. My dealer's owner is a friend in the hobby, and a straight shooter. He has no reason or inclination to B.S. me. I'm not worried at this point. Heck, I placed my order for my '93 Cobra in September '02, and didn't take delivery until June '03!! LOL!! Hope that doesn't happen again! But I've seen my share of delays..
My '88 GT convertible was held-up due to problems with the convertible tops, so it got set to the side with a bunch of other cars in the same boat (I think it was Cars & Concepts doing the convertible work at the time) with a "hot tag" stuck to the windshield, and it was two months before it finally got it's top installed, and the car finished-up. Luckily, they must have assigned one of their best installers to the cars that were hot-tagged, because my car was delivered new with a top that fit as good as you would expect on a Mercedes. Not a ripple, not a seam out of place.. I knew the ongoing status of my car, because I had a friend within Ford who knew people at Cars & Concepts, so they kept an eye on things for me.
My '93 Cobra... man, what a wait. I waited so long that I wound up buying a brand-X to drive, and my dad wound up taking the Cobra once it finally arrived, and he socked it away. It's still in the wrapper, about 20 miles on it.
'97 Saleen S351, it was delayed for more than 4 months. The excuse was that Saleen could not get supplied with T56 6-speeds, because Viper GTS production was sucking the supply-chain dry.
My dad's 2005 Mustang GT was part of that irritating delay on the interior upgrade packages...
Delays happen, especially on 1st-year models. This one appears to be real, and your mention of the Shaker 1,000 possibly being the culprit is news to me, but that could surely be it..