The HAC should tell you whats going on with VSS.
I looked at the HAC from Moates.net for the BDKJ E6 definition file.
It looks like to me that selecting manual transmission (TunerPro RT Constants and Scalars) will either enable the 4L60 (700R4) lockup or enable shift lights. The information below is from the HAC. I did not post the entire HAC just enough to show what I found.
MANUAL & 4L60 TRANSMISSION
* (TH700R4)
* SHIFT LIGHT PARAMS
***************************************************
;--------------------------------------------------
; HIGH ET RATIOS FOR
;
; UPPER ENG RPM/TRANS RPM OF A PAIR USED
; ESTABLISH CORRECT GEAR RANGE FOR SPECIFIED GEAR
; TO ESTAB SHIFT LIGHT TRIP POINT
;--------------------------------------------------
;--------------------------------------------------
; TRANSMISSION LOCK UP CALIBRATIONS
;
;--------------------------------------------------
L5148 FCB 140 ; 65 Deg c, LOWR TCC TEMP LMT
L5149 FCB 5 ; 2% TPS HYST FOR COAST 1 & 2
;----------------------
; TCC TPS Un-lk window
;----------------------
L514A FCB 54 ; 21% NEG DIFF TPS UN-LK LMT
L514B FCB 45 ; 17.6% POS DIFF TPS UN-LK LMT
;
L514C FCB 20 ; 2 SEC DLY LOCK DELAY AFER QUALS
L514D FCB 25 ; 2.5 SEC COAST DELAY
;---------------------------
; TCC LK/UN LK THRESH PAIRS
;---------------------------
L514E FCB 82 ; 82 MPH, TCC LK/UN LK UPPER THRESH
L514F FCB 79 ; 79 MPH, TCC LK/UN LK LOWER THRESH
L5150 FCB 0 ; 0 RPM, TCC LK/UN LK LOWER THRESH
L5151 FCB 0 ; 0 RPM, TCC LK/UN LK UPPER THRESH
;-------------------------
;-------------------------
; TCC RD SPD LMTS PAIRS
;-------------------------
L5152 FCB 30 ; 30 MPH UPPER FOR LK
L5153 FCB 28 ; 28 MPH LOWER FOR UN-LK
L5154 FCB 35 ; 35 MPH UPPER FOR LK
L5155 FCB 33 ; 33 MPH LOWER FOR UN-LK
;--------------------------------------------------
I think the bottom line will be the $$$: I'll program an E6 27SF512 chip using my Burn 2 for a 4.3 using manual transmission. I can't find a neutral / park input for the 16168625 ... so I'll try my luck without the VSS ... if I have problems ... I guess I'll throw $$$ at the problem for a VSS.
I've also looked at IAC Calibrations ... I'm sure the VSS is there somewhere

, but I'm not sure.
****************************************************
* IAC CALIBRATION
*
* TYPE $E6 ECM
****************************************************
dave w