Fairly simple.
Open the video, select file, append AVI segment, load part 2, do the same for part 3 (and 4, depending on which version you downloaded).
Click Video, filters, add, MSU subtitle and logo filter.
Click Configure.
Change to subtitles, set the X and Y position of the timer.
Check to see if you have it correct.
Maybe an easier one to use, would be called "logoaway" (google it).
It has a realtime preview screen, which helps.
Another good one, called "Region Remove" by Shawn Faulds (again, google it), is very simple to use, but doesn't give as good results as the first two.
You have saved it as an uncompressed AVI, which is why it's so big.
I encode (by frameserving) usually with Canopus Procoder Express, or Mainconcept, but you could also use something like TMPGEnc, or make it simpler with VSO DivX to DVD.
