Hello, and welcome to the site. You'll find lots of good people here, and lots of information. If you don't mind me asking, whereabouts are you located?
Judging by the photos that you've posted, you have found a pretty decent car. I've had 3 of these cars in the past 20 years or so. I have one now, and I'm trying to figure out how to fix it up as well. Just so you know, the glass in the rear doors was fixed on all '78-'83 Malibu 4 doors and wagons. The '81 and up 4 door cars had the small vent windows that could be opened, as did the wagons.
Basically, its up to you how you go about fixing up the car. The bellhousing on the existing 229 V6 will bolt right up to the earlier small block and big block Chev V8s, although if you're looking at installing a high horsepower engine, a scattersheild would probably be a wise choice. The 3 speed transmission will work too, but once again, probably not the best choice behind an engine with more power. The stock bellhousing will accept most older GM 4 speed and some of the 5 speed trannys, or you can go aftermarket. The clutch linkage is mechanical, and if you're looking at a V8 swap with headers, be sure to check for interferance between the headers and clutch linkage. Some header manufacturers do make headers to clear the mechanical clutch linkage.
As for the rest of the car, pretty much the sky is the limit, in terms of modifications. Most, if not all of the better steering and suspension pieces from the later G body cars (Monte SS, Buick GN, Olds 442, etc) should fit with no problems. As for the interior, pretty much the same story. If you want to upgrade from the bench seat to buckets, you'll need to install the center floor mounting brackets for bucket seats. Same for a console.
Hope this helps. Keep us up to date with your progress. Good Luck!