I converted my Malibu to manual brakes last August (2000). Take a look at the pictures that I have attached, and try to follow along with my rambling directions. As you noted, insuring that the push rod could not fall out was a primary concern. Some Malibus were sold new with manual brakes, but I have never seen one in a junk yard or otherwise, and the parts are no longer available from GM.  The first thing I did was buy a manual master cylinder at the local Car Quest auto parts store. Next I made a firewall support plate out of 1/8" aluminum. I used the holes in the firewall as a template. This part gets sandwiched between the Master cylinder and the brake pedal bracket. You can see this part in pictures 1, 2, and 4. The next step was to move the pushrod pivot pin on the brake pedal up to the existing hole that is closer to the brake pedal pivot. In picture 2 you can see the pushrod pivot pin in the new location. The open hole in the brake pedal arm was the old location that is used for power brakes. To move the pivot pin I used a grinder to remove the factory peening. I then welded the pin in its new location. Once this pin is moved you can bolt everything together in preparation for measuring the length for the pushrod.  To make a pushrod, I took my old vacuum booster and carefully broke the plastic away from around the pushrod until the pushrod could be removed.  This pushrod will be too long. With the brake pedal, support plate, and master cylinder bolted together, measure the distance from the pushrod pivot pin to the piston in the master cylinder. Cut the pushrod off about 1/8" longer. I then inserted the push rod to check the length more accurately.  Grind, or cut the master cylinder end of the push rod until the pushrod fits well between the brake pedal and the master cylinder piston.  The next thing I did was cut a piece of 1" wide by 1/8" thick steel to serve as a pushrod guide. I drilled a 1/2" hole for the push rod to pass through. I inserted this piece into the brake pedal bracket and inserted the pushrod through the 1/2" hole. You can see the pushrod guide in pictures 3 and 5. You can also see the cut down pushrod. I then bolted the entire assembly together again. If the pushrod guide is positioned properly, the pushrod never actually touches the guide. I then welded the guide in.