You can use any or all of the patches below in your speedruns. You can apply them using any hex editor (e.g., HxD), or you can use this tool that I made instead if you aren't comfortable with that.

All values are in hexadecimal. The original values are given for reference so you can double-check that you're modifying the correct offsets.

Keep the game running when not in focus:

0x13593: 75 -> 71
0x12BC0: 55 -> C3
0x12BF0: 55 -> C3

Make the game window bigger:

This changes the 320x240 windowed mode by multiplying these dimensions by a scale factor. To use this, apply the patch for the scale factor you want and then set the display mode to 320x240 windowed mode in DoConfig.
Note, using this patch may incur a small performance penalty—initial tests indicate that a full Best Ending run may be a few seconds slower with the patch, depending on your computer.

Here is a patch for a 3x size multiplier (960x720):

0xB4A6: 01 -> 03
0xCD6B: 1E -> 10
0xCD7C: C7 45 F8 14 ... -> 6B C8 0A 89 4D F8 6B D0 05 89 55 FC 90 90
0x127C2: 40 01 -> C0 03
0x127CC: F0 00 -> D0 02

This patch scales the window by 4x (1280x960):

0xB4A6: 01 -> 04
0xCD6B: 1E -> 10
0xCD7C: C7 45 F8 14 ... -> 6B C8 0A 89 4D F8 6B D0 05 89 55 FC 90 90
0x127C2: 40 01 -> 00 05
0x127CC: F0 00 -> C0 03

Even higher scale factors are also possible; see this for details.

Automatically advance text when holding Z or X:

Note: If you plan to submit a run using auto text advance, then you must use this patch to do it. Other methods that achieve a similar effect (e.g., turbo buttons) are not allowed.

0x16CA0: 55 8B EC 0F B6 05 ... -> B8 09 5B 4A 00 FE 00 82 38 02 7E 0A C6 05 DC 5A 4A 00 01 C6 00 00 C3
0x25584: 14 -> 10
0x2558A: C6 05 DC 5A 4A 00 01 -> E8 11 17 FF FF 90 90