This is what I can get with Pelle's linker, alignment at 16 bytes, merge data with text and bare minimum code to make a MessageBox run, 768 bytes.
; ¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤
include \masm32\include64\masm64rt.inc
.code
; ¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤
entry_point proc
xor rcx, rcx
mov r9, rcx
lea r8, titl
lea rdx, text
call MessageBox
xor rcx, rcx
call ExitProcess
entry_point endp
; ¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤
text db "How D",0
titl db "Title",0
; ¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤
end
The batch file.
@echo off
set appname=HowD
if exist %appname%.obj del %appname%.obj
if exist %appname%.exe del %appname%.exe
\masm32\bin64\ml64.exe /c %appname%.asm
\masm32\bin64\polink.exe /SUBSYSTEM:WINDOWS /MERGE:.data=.text /MACHINE:X64 /ALIGN:16 /ENTRY:entry_point /nologo /LARGEADDRESSAWARE %appname%.obj
dir %appname%.*
pause
Build your own stub file and you save an extra 64 bytes. 704 bytes and I think its still a legal 64 bit PE.
00000000 :4D 5A 90 00 03 00 00 00 - 04 00 00 00 FF FF 00 00
00000010 :B8 00 00 00 00 00 00 00 - 40 00 00 00 00 00 00 00
00000020 :00 00 00 00 00 00 00 00 - 00 00 00 00 00 00 00 00
00000030 :00 00 00 00 00 00 00 00 - 00 00 00 00 40 00 00 00