I think I can help you here, as I have the exact same set up. On your print side you can print to a max of 27.9", that leaves room for crops in the 4 corners. You will want to change some things in flexi to do that as well. When you click print in Flexi, go to the contour tab in production manager and make sure you have the crop marks set to Graphtec Type 1 automatic. Then click on the options button right next to that and make the changes I show in the picture attached. This will darken the marks so you get less failures on your crop mark scans and make them smaller to get more printable space. Then on the first tab set the position to 0.9" each direction. No need for inches of wasted material. Then when you cut it off you can get away with just 2" on the back side, but only if you make some changes to your cutter.
On the cutter, put tape over the rear sensor to make it think there is always material there. Then you do not need that huge chunk of vinyl they recommend on the back side. Then when you set up the roll you need to trick the machine to think you have a larger roll. I load up some vinyl and push the right wheel over about 1/4" to the right and the left wheel over a whole roller position to the left, that's about 6". Let it cycle and set the size, then move the rollers back into the proper position and instead of choosing "new media", choose "continue", then it will keep the previous settings and think you have 36" media in there. Load up the print like normal and you should not get any errors on the scans.
I hope that helps, PM me if you need any more tips. I have had this same printer and cutter for over 12 years, except my Q series crapped out on me, so I got the newer graphtec, but they are the same as the Q series.