What will I need to replace on my 1995 prelude if a rod is knocking on my si motor?

Replacing the Rod entails tearing your whole motor down, removing the Crankshaft, replacing the Rod Bearings, Rod and Piston and it is not cost -effective to do all that labor for just one Rod. You are better off replacing the whole motor than just fixing the one part. The most cost-effective solution I found that alot of people are doing, is to find a Engine Shop in your area that sells used Japanese Engines Imported from Japan. The engines are used, but only average about 30K miles on them, because in Japan they have very strict Smog and Emission Laws and when a vehicle in Japan reaches 30K miles, they mandatory have to pull out the old motor out and replace it with a new one, which leaves thousands of perfectly good Japanese engines to use as replacements. A good used Motor runs anywhere from $400-600 dollars plus labor, unless you are Mechanically Inclined and you can do the install yourself. I replaced two Hondas and one Ford (Mazda) Festiva motor using this method and never had a problem with them ever.