I compared the tuned flash with a stock 98 and here is what changes the tuner did.
To what I see this was a partial tune and really should be dialed in for the makeup of that car and how you tend to drive it.
Comparison summary: 02:40:18 pm, Monday Feb 04, 2008
{B0105} Wide Open Throttle
CAL: "98" <-> ALT: "100"
{B0701} Catalytic Converter Protection Enable
CAL: "Disable" <-> ALT: "Enable"
{B1201} Abuse Management (in Gear) Upper RPM Threshold
CAL: "9999" <-> ALT: "2000"
{B1207} Abuse Management Vehicle Speed Threshold
CAL: "0" <-> ALT: "255"
{B1209} Abuse Management Time
Different from row 0 to row 15 inclusive.
{B3303} Fuel Cut-off Limiters in Gear
Different from cell: 0,0 to cell: 1,9 inclusive.
{B3618} PE Modifier Based on RPM
Different from row 5 to row 18 inclusive.
{B3605} Commanded Fuel When in Open Loop
Different from cell: 0,0 to cell: 16,12 inclusive.
{B5913} Spark High-Octane Table
Different from cell: 14,14 to cell: 23,16 inclusive.
{B5914} Spark Low-Octane Table
Different from cell: 4,0 to cell: 23,24 inclusive.
{B5908} Fuel Mixture Spark Correction
Different from cell: 0,7 to cell: 19,15 inclusive.
{B5915} Minimum Spark Advance
Different from row 7 to row 20 inclusive.
{B6603} TCS Spark Retard
Different from row 0 to row 19 inclusive.
{B6612} ETC Pedal Torque Limit Reduction
Different from cell: 0,0 to cell: 15,20 inclusive.
{C6001} Engine DTC Processing Enablers
Different from row 2 to row 172 inclusive.
{C5601} Misfire Detection Max Temp
CAL: "1" <-> ALT: "266"
{D1206} WOT Shift Mode Upper Threshold
CAL: "99" <-> ALT: "95"
{D1207} WOT Shift Mode Lower Threshold
CAL: "97" <-> ALT: "85"
{D1208} WOT Shift Mode Upper Threshold - Cruise
CAL: "99" <-> ALT: "95"
{D1209} WOT Shift Mode Lower Threshold - Cruise
CAL: "97" <-> ALT: "85"
{D1210} WOT Shift Mode Upper Threshold - 4WD
CAL: "100" <-> ALT: "95"
{D1211} WOT Shift Mode Lower Threshold - 4WD
CAL: "100" <-> ALT: "85"
{D0901} Part throttle 1->2 Shift Speeds
Different from cell: 0,0 to cell: 3,16 inclusive.
{D0902} Part throttle 2->3 Shift Speeds
Different from cell: 0,0 to cell: 3,16 inclusive.
{D0910} WOT 1->2 Shift Speeds, Normal
CAL: "42" <-> ALT: "40"
{D0911} WOT 1->2 Shift Speeds, Performance
CAL: "42" <-> ALT: "40"
{D0912} WOT 1->2 Shift Speeds, Hot
CAL: "42" <-> ALT: "40"
{D0915} WOT 2->3 Shift Speeds, Normal
CAL: "79" <-> ALT: "77"
{D0916} WOT 2->3 Shift Speeds, Performance
CAL: "79" <-> ALT: "77"
{D0917} WOT 2->3 Shift Speeds, Hot
CAL: "79" <-> ALT: "77"
{D0920} WOT 3->4 Shift Speeds, Normal
CAL: "130" <-> ALT: "134"
{D0921} WOT 3->4 Shift Speeds, Performance
CAL: "130" <-> ALT: "134"
{D0922} WOT 3->4 Shift Speeds, Hot
CAL: "130" <-> ALT: "134"
{D0925} WOT 2->1 Shift Speeds, Normal
CAL: "42" <-> ALT: "35"
{D0926} WOT 2->1 Shift Speeds, Performance
CAL: "42" <-> ALT: "35"
{D0927} WOT 2->1 Shift Speeds, Hot
CAL: "42" <-> ALT: "35"
{D0930} WOT 3->2 Shift Speeds, Normal
CAL: "78" <-> ALT: "73"
{D0931} WOT 3->2 Shift Speeds, Performance
CAL: "78" <-> ALT: "73"
{D0932} WOT 3->2 Shift Speeds, Hot
CAL: "78" <-> ALT: "73"
{D0935} WOT 4->3 Shift Speeds, Normal
CAL: "110" <-> ALT: "134"
{D0936} WOT 4->3 Shift Speeds, Performance
CAL: "110" <-> ALT: "134"
{D0937} WOT 4->3 Shift Speeds, Hot
CAL: "110" <-> ALT: "134"
{D0940} WOT 1->2 Shift RPM, Normal
CAL: "6100" <-> ALT: "6000"
{D0941} WOT 1->2 Shift RPM, Performance
CAL: "6100" <-> ALT: "6000"
{D0942} WOT 1->2 Shift RPM, Hot
CAL: "6100" <-> ALT: "6000"
{D0945} WOT 2->3 Shift RPM, Normal
CAL: "6100" <-> ALT: "5900"
{D0946} WOT 2->3 Shift RPM, Performance
CAL: "6100" <-> ALT: "5900"
{D0947} WOT 2->3 Shift RPM, Hot
CAL: "6100" <-> ALT: "5900"
{D0950} WOT 3->4 Shift RPM, Normal
CAL: "6100" <-> ALT: "5900"
{D0951} WOT 3->4 Shift RPM, Performance
CAL: "6100" <-> ALT: "5900"
{D0952} WOT 3->4 Shift RPM, Hot
CAL: "6100" <-> ALT: "5900"
{D1108} Desired 1-2 Shift Times
Different from cell: 0,0 to cell: 0,16 inclusive.
{D1109} Desired 2-3 Shift Times
Different from cell: 0,0 to cell: 0,16 inclusive.
{D1110} Desired 3-4 Shift Times
Different from cell: 0,0 to cell: 0,16 inclusive.
{D1002} TCC Apply Speeds - Third Gear
Different from cell: 0,0 to cell: 3,16 inclusive.
{D1003} TCC Apply Speeds - Fourth Gear
Different from cell: 0,0 to cell: 3,16 inclusive.
{D1005} TCC Release Speeds - Third Gear
Different from cell: 0,0 to cell: 3,16 inclusive.
{D1006} TCC Release Speeds - Fourth Gear
Different from cell: 0,0 to cell: 3,16 inclusive.
{D1009} TCC Throttle Release - Fourth Gear
Different from cell: 0,0 to cell: 0,16 inclusive.
{D0701} Base Pressure 1->2 Shift
Different from cell: 0,3 to cell: 0,32 inclusive.
{D0702} Base Pressure 2->3 Shift
Different from cell: 0,3 to cell: 0,32 inclusive.
{D0703} Base Pressure 3->4 Shift
Different from cell: 0,1 to cell: 0,32 inclusive.
{D0801} Torque Reduction 1->2 Shift
Different from cell: 0,6 to cell: 0,16 inclusive.
{D0802} Torque Reduction 2->3 Shift
Different from cell: 0,6 to cell: 0,16 inclusive.
{D2001} Abuse Mode RPM Enable
CAL: "5555" <-> ALT: "1200"
{D0301} Transmission Torque Reduction
CAL: "Disable" <-> ALT: "Enable"
{G1201} Anti Theft Configuration
CAL: "None" <-> ALT: "Class-2"
{G0901} Fan #1 Turn-on Temp
CAL: "200" <-> ALT: "226"
{G0902} Fan #1 Turn-off Temp
CAL: "194" <-> ALT: "219"
{G0909} Fan #1 Run-on temp
CAL: "200" <-> ALT: "284"
{G0910} Fan #1 Run-on time
CAL: "30" <-> ALT: "1"
{G0913} Fan #2 Turn-on Temp
CAL: "210" <-> ALT: "235"
{G0914} Fan #2 Turn-off Temp
CAL: "200" <-> ALT: "227"
