According to my Chilton'* 28200 vacuum diagram for 98-99VIN K, the fuel pressure regulator vacuum comes from a tap at the throttle body. The charcoal canister purge valve (where you ask about the connection to the fuel pressure regulator) is only shown with two vacuum lines and an electrical connection in the diagram. One supplies vacuum from the throttle body, the other goes to the canister. In your picture, the hole you indicate on the purge valve appears to have dust in it. Could be just bad lighting, but if a hose had been in that hole, there should not be dust in the bore. Sometimes these generalized (Chilton'*) diagrams are not correct, so check on the inside of the hood and radiator support for a vacuum diagram specific to that vehicle. I use a silver sharpie to mark the lines when I disconnect them; you might want to throw one in your tool box for next time.
The fuel rail leaks are probably caused by bad o-rings in the female part of the connector that you removed from the rail. Make sure you get fuel-rated o-rings the right size to replace them. The dealer should be a good bet for those. They are difficult to get in and out, but it can be done.
Speedy wash will clean the lower intake manifold, but probably get you filthy in the process. Another option is to buy a gallon of kerosene and pour it into an oil drain pan. Get a stiff parts cleaning brush and go to it. Don't use abrasives on the gasket sealing surfaces. Use a razor blade holder with a single-edge blade and/or a good carbide edge gasket scraper. Be careful to keep the carbide and razor flat, and change the blade when it gets nicked to prevent scratching the aluminum.
NGK TR55 plugs will make the car very happy.
We just learned that the newest Dorman UIM kits are supplied with a reduced diameter stovepipe that will fit the 95-98 LIMs. If you are going that way instead of the APN (a better choice) try to find one of these newest stock items. You don't want to put this together with the stock 3/4" stovepipe. The Dorman kit will come with new o-rings for the injectors. A little silicone on those o-rings will help that rail to pop right back into the LIM.
When you upload your images, if you can, resize them to 600 pixels wide so everyone does not have to scroll left and right to read the thread.