Whoever said put a D16Y8 in it, don't put a D16Y8 in it. LOL. I just did that to my CRX and zomg what a pain in the ass that was.
Welding the new metal in shouldn't really be that hard. Just get a mig and practice to the side with some scrap metal and then cut/tack/weld your new piece in. You cut it out and ground out the rust, might as well as just finish it up now ya know? You can always use body filler to smooth out the imperfections, that's what it's good for.
As far as the manual swap goes, really the only thing you'll need is the third pedal, clutch cable, a transmission and new rear/side mounts, and a shifter/shift linkage. All of which can be had for next to nothing at the junkyard.
There should be previsions for the third pedal under the dashboard already there, and I'm sure there are bolt holes for the shift linkage, but I'm not sure.