Evilheart: Part of your problem is that the emulator is only outputting 224 lines, but your script (which looks to be based off mine that I posted on Doom9) is assuming that the emulator is outputting a 240 line video. Two ways to fix this - either set FCEU up to output 240 lines in NTSC mode (in the Video options, there are settings for first and last scanline in both NTSC and PAL - set the top scanline to 0 and the bottom one to 239), or change the fourth through sixth lines of your script to read as follows:
PointResize(512,224) # omit this for softer vertical transitions
BilinearResize(650,224)
AddBorders(35,8,35,8)
The second method will hide any garbage that may exist on the top or bottom 8 lines.
The field order shouldn't be that much of an issue - as far as I understand, NTSC DVD is primarily top-field first (it's NTSC DV that is BFF).
jdurg: What type of audio did you use? AC3 (Dolby Digital) is notorious for having an incorrect audio level when not set up properly, due to things like "dialog normalization". Unfortunately, such audio issues are outside my current scope, but it's something that I am constantly trying to learn. As for interlacing the SM run properly, you might try using a variant of my NES Avisynth script, such as this (untested, but should be a good starting point):
AVISource("nesoutput.avi")
AssumeFieldBased()
AssumeTFF()
PointResize(512,240) # omit this for softer vertical transitions
BilinearResize(650,240)
AddBorders(35,0,35,0)
Weave()
AssumeFPS(30000,1001,true)
If your generated AVI is 224 lines, then make the same modifications that I recommended to Evilheart. Unless there is some audio skew in the SNES emulator output like there is with FCEU, then this should work for you.