I got the old pads off but cannot get the caliper back on. The rod will not go back into the rubber boot.

By Rod, I assume you mean the caliper piston?

1.Look on the casting area for the caliper piston. There is a bleeder valve. Has a hexagonal shape on it, that you use a box-end wrench to loosen, or tighten it. This bleeder valve needs to be open.
Turn to the Left, (Counter-clockwise) to open.

If we are indeed referring to a 1999 model of vehicle, be aware that it is 10 years old, and the bleeder valve May have rust, or corrosion on it. This results in a little difficulty, in applying the box end of the wrench, over the hexagonal nut shape of the bleeder valve. Line the box end of the wrench up, with the flats of the nut shape.
Use finesse, and lightly tap the wrench down over the nut shape, with a small hammer. To remove the wrench, wiggle it as you are taking it off.
It also may be difficult to turn.

I realize all of the above 'sounds' easy, and it will be a little more difficult. I thought I would add a tip to try to help.

You should have a container under the caliper, to catch the brake fluid as it drips out.

2.You need to compress the caliper piston back into the caliper.
As the brake pad wore, the piston came out further to make up the distance.
Now the piston needs to be compressed back in, for the thickness of the new brake pad.

You can use a large C-clamp to do this, or more advisable, is to purchase the correct tool from your nearest auto parts store. This tool is relatively inexpensive.

ADVISEMENT!
The bleeder valve should be open, before compressing the caliper piston back into the caliper piston bore.
If you do not have the bleeder valve open, you will push junk through the brake line, and up into the brake master cylinder!
Always have the bleeder valve open!

Moisture is present in the air. As an object, like a brake master cylinder for example, heats up then cools down, moisture develops in droplets, and goes to the bottom of the master cylinder reservoir. It then starts to develop rust.

This rust will go down the orifice hole, at the bottom of the master cylinder's reservoir, and into the master cylinder's components. Then down through the brake line/s to the caliper/s.

When replacing the brake pads, you should drain all of the brake fluid out, and wipe the master cylinder reservoir out with a clean, lint free rag. Then after the brake pad/s are replaced, fill the master cylinder reservoir with new brake fluid.

When you bleed the brakes, you will have clean brake fluid in your brake system, and help your brake system to last longer.

Im not understanding the rod term. Do you mean the "ROD" or the "PISTON"? back into the rubber boot. Big C clamp is best tool to use to force the piston back into the boots, you might have to open the bleeder valve to help release some of the pressure but make sure your resevior is full of brake fluid, if you have ABS systems do not the fluid run empty and you will have more problems when trying to get air out of the unit and there are special way to bleed the ABS systems. depending how far the piston has came out from your caliper, if it came out beyond the point of the rubber seal, your in trouble and definitely will not able to push piston back in the caliper, you might as well get a rebuilt one. If it has not come completely out than your fine it stubborn and require lots of effort. repost if we are not talking about the same rod/piston.

You will need a larger sized C clamp to slowly push the caliper back into its boot. Make sure your brake fluid reservoir kid is OFF,..allowing for the fluid to go back into the reservoir. Once you have placed the C clamp around the caliper, take an old brake pad and place it across the round piston...place part of the clamp over this pad and tighten the clamp..Do not place the clamp directly on the piston, you may damage it or compress it in crooked. so place a used pad across it. Push the piston back in untill its almost flush with the boot, making sure no dirt is on the silver exposed piston..u dont want dirt to go back inside the boot. Once its in, refit the caliper to its mount with the new pads.