By all means, follow the instructions! Trim down the perimeter until the gap over the roll bar is close. If you don't, then a gap will occur as the ends are high and the center drops. I used an angle head die grinder for the big cut. When making the big cut, a frame to keep it from spreading and/or dropping is good to prevent stress on the cut as it progresses. I also taped behind the cut periodically.
After the big cut, I made a cradle to hold the canopy upside down in order to use the various tools for fitting. I made three hoops from 2X4's then feet with carpet for the cradle. Kinda like a boat trailer, only with more contacts. A diamond wheel in a dremel makes nice precision cuts for trimming. I sanded with a belt sander for part, but used a 18" board with sand paper for the hoop edge to keep it planar. Get a number of grits of sand paper on blocks ready, so you can keep the edges relatively smooth thus avoiding a crack.
Good Luck, it is a lot more talk than action with the big cut. It only took about an hour. Fitting is much longer.