Well since youhave upgraded the SEPM to mr4 and all your clients are still at RTM version ( 11.0.780 ) I don't think autoupgrade would work in this case.
But what i can suggest is think as a fresh install.
Export a Client install package with the setting of "Remove previous logs and settings and reset- Client-Server communication"
and push out this package either via Migration or deployment or find unmanaged computers and all your clients should be fine.
We used this back then and it used to work great.
Once all your clients are at MR4 without any leftovers of RTM then MR4Mp2 and future releases should be a cake.
As far as Content folder is concerned from MR3 onwards that issue was fixed so now you need not worry about then content folder at the max it will reach 1 gb.
That too it is configurable ( no. of content revisions to keep)
Admin - Servers- Local Site ( My Site ) - Properties -liveupdate -Disk Space Management for downloads