Made a write up in the YJ technical section on how to drain and clean the inside of your frame to prevent rust so im just going to copy and paste it here. This is a good "mod" for anyone living in the rust belt or does a lot of driving in the mud.
Why: Why would you drill holes in your frame you ask? Well b/c your Jeep came from the factory with a bunch of holes cut out in your frame for access to bolts and what not. Over time mud, dirt, salt water and what ever else your tires kick up end up flying into those holes and finding a resting place in your frame. The mud and dirt will get packed into the flat spots and crevasses of the frame then when it rains or you drive your jeep through water, the water gets trapped in the the dirt and mud that is sitting in your frame. Now that you have a frame packed with mud and I mean packed, There's no way for that water to escape therefor rotting your frame out. The drain holes allow you to wash out that mud and water by sticking a hose or pressure washer through the factory frame holes and allowing drainage to occur out of the newly drilled drain holes.
2. 1/4" or similar sized drill bit
3. Step drill bit or tapered bit
4. chassis paint of some sort
5. Hose or best, Pressure washer
6. Air compressor
Locate where you will be drilling your holes. I found that the best places to drill holes are in the flat areas of the frame, where grim can get trapped.
Start with your 1/4" or like Drill bit, this way you have a good guide hole and wont risk wrecking your pricy step bit.
Start your first hole at the very back of your frame behind the shackles. Drill the hole about an half inch From the rear cross member.
Once you have your guide hole drilled, switch to your step bit and drill the hole out to 3/4"-1" hole. Once you have a nice 3/4"-1" hole repeat the process on the other frame rail.
Now move up on the frame some to just in behind of the rear spring hanger. Repeat the same process as you did at the rear shackles, Start with small guide drill bit then use the step bit to make the 1" hole.
Now your on to your last two holes, one on each side of the frame. These will be drilled just behind the front spring hanger in the same spot as you did to the rear, just up front.
Now as you were drilling I'm sure you noticed that there was about an 1" thick of mud and dirt packed onto the bottom of your frame, now you finally get to get that crap out!
By using the factory holes in the sides and tops of your frame rails you are going to spray water into the frame, its best to use a power washer or a high pressure hose and start from the front and move toward the back. Once you start spraying water into your frame you will notice your newly drilled drained holes will start spewing nasty brown water, this is good and means you are getting the gunk out. If you don't see any water coming from the drain holes or very little this means you have a major plug and need more water pressure or need to stick something up into the frame to get the water flowing through.
You can also spray water up through the drain holes which works well for getting the mud that pack in the flat spots of the frame.
Once you get to the back of the frame and around the rear shackles, you really need to wash that area out well. The rear shackle area of the frame is most prone to rot and holds the most mud and water. You will probably have to poke a screw driver or like object up through the drain hole to get the mud loose and use a lot of water pressure. It took me a good 20 min of spraying and poking to get the shackle area of the frame clean.
Once you no longer see dirty water flowing from the drain holes and the water is clear you can stop spraying. Now, take your air compressor and spray out any loose crap that didn't get washed out with the water. You might also have to re rinse your frame out with the hose after spraying with the air. Repeat the washing process until you are happy with how clean the frame is.
This is what came out of my frame, about 50 pounds of dirt and mud, mouse nests, leafs and some other unknown stuff, well worth drilling six holes in my frame if you ask me!
Make sure once the frame is dry that you paint the bare metal holes with a good chassis paint to prevent any rust. Now that your frame is clear and water flows out the drain holes well you can stick a hose in the frame once or twice a month or every time you wash your jeep to keep the frame clean and rot free!