PVC piping and a plastic pipe to wall were connected before but then water stopped flowing all of a sudden. I thought it was due to clogs and I cleaned it all out. I can connect it back (not sure if it was the same way as before) but water won't flow uphill anymore like before. Water just sits in the J part of the first pipe.

When I took the pipes off there was a metal rod inside the pipes, and I wasn't sure what that was for. I had to replace some of the pipes because of mold.

http://i.imgur.com/SCUBn5o.jpg

http://i.imgur.com/cIGqDQ9.jpg

If anyone could help with suggesting how it can be water flowing up like it did before that'd be great. Thanks.

" but water won't flow uphill anymore like before" Against the law of Physics. Water won't flow up. If you can get the tailpiece connector flush against the sink, it may work. I can't imagine it worked before, or at least not well. Based on the picture angle in #2, water will be at the drain level. Try reversing the trap, see if that helps.