-Delete the first 16 ines header bytes with hex editor.
-Cut the last 4096 bytes out of the nes file with hex editor and duplicate in a new file twice so that I have 8Kbytes of chr data.
-Fill the rest of the NES file with 0s until it equals exactly 32 KB.
-Burn the 32 KB nes file onto prg chip and 8 KB chr binary file onto chr chip.
1. Yeah, the header's got to go. The header was only meant to take the place of cartridge internals, anyway.
2. Why don't you cut everything else out, and then duplicate it in a new file twice? And how come you only have 4k of chr data anyway?
3. Filling it in with FFs will make it burn faster. But yeah, the prg data should be exactly 32K, if that's the size of eprom you're working with.
4. That sounds about right.
I hope this helps.
Be whatever the situation demands.