You got a sweet ride.
I would keep it and do the new alarm when you get a chance. There are very few Bonnevilles that look as tight as yours.
Besides, if the alarm isn't working right it will probably bother you every time you go to use it (it would bother me). If you got the CTS you would be starting from scratch again. The choice is ultimatley up to you.
So what exactly did they mess up on? Don't the extra features work right? If the shop messed up or did a poor job can't you get them to fix it?