Real life is pretty much guess work aswell, it's not like most people have the money to strip their car multiple times adding more and more seam-welding until the chassis is as stiff as you need.
You just have to strip it, add as much chassis mods as you think you need, and hope you got it right. If you add too much, there's nothing you can do about it. If you add too little, you won't realise until you are back out on track and by then, you're looking at another full strip and rebuild to add more. It's a LONG job, especially when you add in the fact you'll also have to strip all the seam sealer off the joins prior to welding, prep the metal, and then respray afterwards.
Most people will just fully stiffen the chassis and then soften off the suspension to compensate if it's a little too stiff. I'd imagine GT5 is the same, stiffen the chassis, soften the suspension.