SUCCESS!!!! 
I posted this same solution on this thread:
http://forum.arcadecontrols.com/index.php/topic,130016.0.htmlBetween trying to understand Pre/Post command structure here (Thank you drventure!!) and AHK scripting along with how Howard_Casto's wrapper worked in the other (Thanks to nitz, Howard_Casto and BadMouth), I finally figured out how to do it.
Perhaps there's another way to do what I was trying to do but for me it involved using the Pre/Post Commands in Mala along with a carefully crafted AHK script. All this to keep the functionality of Howard's excellent VP wrapper intact (and not loose focus) while still being able to add a bit more functionality for my X-Arcade tankstick. I also wanted to keep with my consistent 2 button exit format along with the rest of the emulators on my arcade cabinet.
Now the SOLUTION!!
First I tweaked my AHK script (VPControls.ahk) for the Pre-Command in Mala. I suppose I could have compiled it to be an .exe, but the simple .ahk format ended up working just fine:
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SetWorkingDir, C:\Arcade\Visual Pinball\
#SingleInstance force
~LButton::g ; Nudge Right remap. The "~" is required. Otherwise focus is lost on some tables. Somehow V.P. "clicks" left on tables to begin.
~LButton::d ; Nudge Left Control remap
~2 & ~4::
Send {Esc DOWN} ; Esc key MUST be held for for a bit in order to register with the wrapper. Thanks Howard for the head up.
Sleep 1000 ; keeps the Esc key down for one second
Send {Esc UP}
Sleep 500 ; putting in this small pause seemed to help
ExitApp ; Closing AutoHotKey.exe here rather than in the Post command proved to be possible after all.
return
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Then I set up Mala as follows so Howard's wrapper and the AHK script would play nice together. Pre/Post commands were the vital parts:
EXECUTION TAB
Pre Command:
cmd /c start "" "C:\Arcade\Visual Pinball\VPControls.ahk"
Command line (same as always):
"%rom%.%ext%"
Post Command:
(NONE/EMPTY - Not needed because I set up the closing of the ahk script within the script itself)
BASICS TAB (same as always to launch Howard's wrapper):
Executable (keeping the wrapper as the launcher):
C:\Arcade\Visual Pinball\vp-launch6.exe
Rom Path
C:\Arcade\Visual Pinball\Tables
Rom Extensions:
vpt
And that's it!! From Mala/Visual Pinball I can launch any table from the menu. The ahk script sets a few controls I couldn't remap otherwise and stays running in the background. Mala then launches Howard's excellent wrapper (vp-launch6.exe). The wrapper takes control of Visual Pinball and plays the table accordingly WITH the added controls of the ahk script. There is no conflicts or loss of focus. I can nudge using the 2nd flipper buttons now on my X-Arcade!! Then, when I'm done playing that particular table I press the 2+4 buttons together (on my X-arcade, not keyboard) and BAM! I'm back to the Mala menu and BOTH Visual Pinball AND AutoHotkey.exe have been closed!!! I tested this over and over on many different tables. Works like a champ.
I hope this thread helps someone else with a similar goal in mind.
Thanks again everyone who chimed in on this thread (drventure, BadMouth, Gray_Area, PaTrYcK). Thanks for your help and knowledge.