Sounds like you've made a lot of good progress. That's great that the wheels only stick out an inch. Mine stuck out about an inch before I widened the fenders. It didn't look too bad. It actually made it look kind of tough but I want the fenders to cover the wheels so I can drop it as low as possible.
As for the heater channels go, I will box them off where I cut them so the body could drop around the frame. The way I did mine was I welded some angle iron mounts rails for the body to bolt up to.
And I used angle iron for the floor / seat support which was also welded to the frame.
Last, but not least I used some angle iron for the gas tank mount which is also functioning as a rear body mount which will bolt to the former firewall, or what's left of it.
Angle iron is free here at work.
Nothing super fancy, but serves it's purpose. Forgot to mention the 1/8" x 6" x 6" plates I welded to the frame which will sandwich the flooring I'm going to build and that'll act as some more body mounts. Plates are so I can weld the roll bar / cage to them and still be able to remove the body.
Basically I want the body to be able to unbolt just like the body originally could be unbolted from its pan. I haven't built the flooring / firewall yet cause I still need to rebuild the motor and trans, and then install them so I can make the floor / firewall. All which is being held up by the finishing of the frame.
The reason I'm doing it this way is cause my limited space in a one car garage apartment. I only want to have to install the drive train once. The flooring and firewall will be a piece of cake though.