Startup tune for a new motor

I have a 2000 FRC Corvette. When I bought the car it had 20 inch rims on it, an SLP Loud Mouth cat back system, and a Mid West Corvette twin filter cold air induction system on it. I'm pretty sure it had been "tuned" in some way as the speedo was right on and obviously the tires were much taller than stock. Since I've had the car I have done several modifications to the suspension, the brakes and chassis, as well as adding a better flowing power duct, a LS6 instake with the included 28lb injectors, 1 3/4 long tubes and an X pipe back to the cat back system. I then purchased EFI Live with FSV2 and sent the current tune in the car off to a mail order tune house that made adjustments for the mods I added. Once I received the modified tune back I flashed it into my PCM and drove the car a bunch. Over the last few years I've been collecting parts and assembling a stroked LS3 motor to put into the car. Not sure how specific you guys want me to be about the components on the motor but this is what I've got. I bought a brand new LS3 block from Scoggin Dickey. It has a Callies Magnum 4.0 inch stroke crank with Callies Ultra rods. It has J & E assymetrical pistons with a zero deck height and a 11cc dish. Heads are the Trick FLow Gen X CNC model that were setup by Total Engine Airflow with Titanium retainers and Manley springs that I wanted installed. The cam was a special order grind that you can spec through Comp Cams. You pick through sets of lobe profiles, specify the LSA, etc.. The specs are, Intake is 283 duration @ 0.050 w/ 0.598 lift with a 1.7 rocker, Exhaust is 291 duration @ 0.050 w/ 0.610 lift with a 1.7 rocker, the lobe seperation angle is 111 degrees, and there is 3 degrees of advance ground into the cam. Morel short travel lifters and Manton pushrods. The rockers are Yella Terra 1.85's. It has a Fast 102mm intake and, a Nick Williams 102mm DBW throttle body. The CAI system is a Halltech Super Bee 2 that uses the late model Hitachi G8 MAF sensor. It has MSD (non multi spark) coils and Deatsch Werks LS3 style injectors that flow 48.2 lb/hr @ 58psi. All the sensors are new. The Callies crank has a 24 tooth wheel on it and I have the conversion wiring for all of it. I have no idea if any emissions controls, or VATS, etc.. have been disabled. So I downloaded a stock tune from the repository for my car. I'll do a compare with the tune currently in the car to do the stuff like the speedo, etc.. I have converted the data from Deatsch Werks (that was in HP format) to EFI Live and input it into the stock tune. It was flow rate vs delta pressure, injector offset vs delta pressure vs ignition voltage, the short pulse adder table, and the minimum injector pulse width. Are there other tables I'm missing to model the injectors properly? Do I modify the basic parameters of the motor in the software to match the new motor (like size in liters, etc) ? I received a Excel spreadsheet from the place I purchased the Super Bee from that Lingenfelter Performance produced. They sell a 100mm MAF that uses the same Hitachi slot style sensor and the Super Bee is that diameter inside as well. The spreadsheet is titled C5 conversion table Delphi 85 to Hitachi G8 MAF, and it has airflow values at various Hz frequencies. I think my year of Vette has a 78mm MAF. Should I just enter the values in EFI ? Does it matter that my car had a 78mm MAF and the conversion table is for the 2001 and up 85mm ? Shouldn't the table just represent the amount of airflow through a 100mm tube measured for a corresponding frequency ? I have a motor sim program that gives a calculated VE number (as well as a ton of other stuff) and I have the exact cam specs in it, the flow bench results for my heads at various valve lift points, etc.. all of it is pretty specific. Should I consider using the VE values from it to start out with ? I've saved links to several pages that I believe relate to my scenario, such as throttle body resizing and the like. Are there any good tutorials on removing/disabling emission controls ? I'm sure I will need help with my Calc Pids and what to start with as far as tuning goes (i.e. Auto VE, or...) once the motor is installed. I guess what I'm asking for ATM is help with getting something pieced together enough to get the car started and start breaking in the new motor. Sorry about the length of this one, and as always any help is much appreciated.

Wow what a large camshaft I have !! Those duration figures in my previous post are advertised total duration not @ 0.050. The correct numbers are Intake 234 @ 0.050 and Exhaust 242 @ 0.050

Just a little bit of difference there!