I believe XTM Nitro X-cellerators comes with pullstart motors as stock, and because of that the engine mount is higher to fit the pull start assembly. You will need to get a non-pull start motor mount to lower the engine and the flywheel. Or if you have the right tools you can just cut your motor mounts to the height you needed.

It also helps to enlarge the hole on the chassis to fit large bump wheels of starter boxes.