i find your rambling and endless string of questions quite exhausting so didn't read this in its entirety. but here's your "short & sweet" answers:
1-a 2004 and later XL and/or XR motor will NOT fit into your M2 frame without major and i mean major fiddling. bottom mounts about spot-on but other than that be prepared for extensive fabrication/wiring/plumbing mods.
2-2004 and up XL/XR motors rubber mounted and completely different mounting points and fasteners than all previous years.
3-fitting an XL883 motor into a Buell M2 is just plain dumb.
4- pre-2004 XL motor frame mounting points match your M2 frame both at the rear and top. but still requires some light-to-medium fab work to complete the installation.
5-this really is NOT the forum for a potential project like you are considering. XLFORUM.NET is along with a few others. google is your friend.....and this.........
https://www.hdforums.com/forum/sportster-models/744688-m2-cyclone-engine-transmission-into-a-90-sportster-frame.html