Short answer: Don't mess with the airbox on these bikes. They are VERY sensitive to airbox changes. Put a K&N filter in there, and do nothing else. You might luck out and find a Kerker for a VF500F Interceptor, which you can modify to fit the magna. In that case, you'd want to go up one main jet size and possibly shim the needles. However, if you're just running slip-ons on the stock collector, as shown in your pics, leave the carbs with the stock jetting. I must reiterate, under no circumstances modify the stock airbox. It's been tried. It always results in less power. Always. It makes fitting a different tank difficult, but trust me on this one.
You can't fit a CB motor in that frame. And you don't want to either. The V4 is a better motor, and the V30 is really quite a fun motor. It's geared for a stupid top speed, which you cannot attain with those 500ccs in there. I had problems pulling past 80 in 5th gear - much less 6th - with a bone stock bike in a good state of tune. It'd do the ton, but it took forever. That said, it'd do 85 topped out in 4th, so it was slow due to gearing more than anything else. Go with the smallest front sprocket and biggest rear sprocket you can find. Added benefit: The bike will now want to wheelie. A lot. And you get to experiment and find out what the actual top speed is!
Good luck!
Charles.