I don't think there is a way to control config.sys, but you can use the sleep.exe (comes on resource toolkits for 98,NT4,2K) in the autoexec.bat to pause for x number of seconds before continuing.
If you don't have access to a resource kit, let me know and I can email it to you.
I also found this script you can use (it is setup for minutes) in the BAT file:
@echo off
REM ** Delay is set to 5 minutes
set delay=5
set testtime=%time%
if "%testtime:~0,1%"==" " set testtime=0%testtime:~1%
echo Start time: %testtime:~0,8%
set /A hh=1%testtime:~0,2% - 100
set /A mm=1%testtime:~3,2% + %delay% - 100
set ss=%testtime:~6,2%
if /I not %mm% GEQ 60 goto NORMALIZE
set /A hh=hh+1
if /I %hh% GTR 23 set hh=0
set /A mm=mm%60
:NORMALIZE
if /I %hh% LSS 10 set hh=0%hh%
if /I %mm% LSS 10 set mm=0%mm%
echo Waiting for: %hh%:%mm%:%ss%
:TIMETEST
set testtime=%time%
if "%testtime:~0,1%"==" " set testtime=0%testtime:~1%
if not %testtime:~0,2%==%hh% goto TIMETEST
if not %testtime:~3,2%==%mm% goto TIMETEST
:SECTEST
if /I 1%time:~6,2% LSS 1%ss% goto SECTEST
echo %delay% minute(s) has gone by
set testtime=%time%
if "%testtime:~0,1%"==" " set testtime=0%testtime:~1%
echo End time: %testtime%
set testtime=
set delay=
set hh=
set mm=
set ss=