Those fittings hitting the rail are for hooking up a heater core. You can run this unless you plan to have a heater.
https://www.amazon.com/dp/B000C2U8Q2/?tag=hardlinecrawlers-20
Weld the tube all the way around.
I like it, reminds me of when I got started. Your drawing seems different than what your building. To me there's way too much tubing in the drawing. But I'm nobody and nothing special so take that with a grain of salt. With that said what size tube are you...
Not that it will help now but I had a buddy machine alum spacers to use instead of the bushing. One thing I did before the spacers was use urthane bushing grease on them to help when taking apart.
You can take another middle piece or bolt and press the tube out until you can grab with pliers...