05 Vibe transmission and windshield water leak

Not long after I bought my 05 Vibe I noticed that water leaks onto the passenger side floor and soaks my carpet when it rains. I tore up the carpet and all of the floor plugs are in. Any ideas? Also my check engine light just came on and the diagnostic said that it had something to do with fuel flow so maybe fuel filter? Lastly my Automatic tranny also just started to shift hard more so from 1st to 2nd gear. Any help would be great.

Water on the floor could be coming from condensation in the heater box, or a blocked drain from the area in front of the windscreen. If you park under trees, I would put money on the blocked drain. If you have a sun roof it can also have blocked drains and it could be coming from there.