Well that's not going to work.
But it's good that you're experimenting yourself.
I don't know what $99 and $9D refer to here but I assume it's the address on the pattern table for part of the characters (I assume the two characters use more than one 8x8 tile).
The easiest method would be to literally copy-paste the characters over each other in Tile Molester: no hacking knowledge required, but somehow I think it'd defeat the purpose of experimenting.
If you want to change the actual reference, you'll have to get into the code, so we're talking assembly. It's not as scary as you might think, but you won't find it by simply searching the ROM for $99, as you'll find thousands of results ($99 is quite a common opcode for an assembly instruction).
I'll have a look later today and see if I can figure out what you're looking for.
EDIT: Okay, I've had a look, and I have some success.
I'll give you the short explanation of what to do, then how I did it.
Open a hex editor like HxC and change:
$6EEB to 9C
$6EED to 98
$6FB7 to 00
$6FB9 to 02
Right, now the explanation of how I found that.
Opened FCEUX's PPU Viewer and saw the two tiles for the old man at $98 and $99 (Zelda uses 8x16 sprite mode, so they count as a single sprite). The game takes those two tiles (one sprite) and flips them horizontally for the other half of him. So to see why the game picked $98 for the old man, we need to use the Trace Logger.
Using save states, I get to the frame directly before the old man appears on-screen, turn on Trace Logger (to a file), advance one single frame, then turn off the Trace Logger. This gives me a file with everything the CPU did in that one frame - it's a lot, but it definitely found that $98 in that frame. I look in the RAM at that moment at $200-300 and search for $98. I see it in there twice - one for the left side, one for the right. You'll need to read about PPU OAM to understand what the $200-300 area of memory actually means:http://wiki.nesdev.com/w/index.php/PPU_OAM
Anyway, I find the exact RAM address where $98 gets sent to, and search for it in the log file. I see an instruction at $788D: STA $0201,X @ $0289 = #$98. This tells the CPU to store the contents of the Accumulator to address $289 (your number may vary as it's cycled around the $200-300 range), the contents of which is $98, obviously. So I then search backwards for #$98 to see where that came from, hoping for something between $6000-FFFF (meaning it came from the ROM).
I see it was stored to $0002 in RAM, but it got there from $766B - bingo. Now, the $6000-7FFF portion of NES address space isn't actually ROM, it's cartridge SRAM - where the games are saved for later. People think SRAM is just for saving games, but in fact it's simply extra RAM which can keep its state with a constant power source - like a battery - whereas the RAM in the NES will lose its data if it's not constantly refreshed. So the game took this $98 from the ROM and wrote it to the SRAM. So where is it in the ROM? Let's right-click $766B in the RAM window, and make a write breakpoint, then reset the game.
As the NES boots, it will write $98 to $766B, and we can now see that it comes from $AEDB in the NES address space. So go to $AEDB in the RAM window, right-click, "go here in ROM file", and there's your result: $6EEB. As for the other two numbers, that's to select the palette, because the old man and the trader use different palettes. I found those numbers the exact same way.
So there you have it. Of course I have a lot of experience with the NES and 6502 assembly, but if I can figure it out, so can you. Hope this was educational for you!