It can also be rebuilt with heavy duty steel/friction plates, which are thinner and stronger, give the clutch packs more grabbing force. There are a few companies out there that will build track ready 4T80E's. They aren't cheap though, so to build one up for a daily driver would be useless. They can be built to handle well over 600+hp, and at least 500+ lb/ft of torque. Such a transmission would really only be at home in something like a Fiero where you could apply F/I to the N*, making it necessary to build the tranny up, otherwise you'd toast the clutch packs anytime you tried to shift passed 70% throttle. That's why Mark would shift at red line, the clutch packs would have just slipped and fried themselves. You'd also probably need some stronger planetary gears sets as well. These could be machined, but would be costly too. With the clutch packs grabbing a hold of 500+lb/ft of torque, the stock gears are likely to simply shear teeth off, or just crack and explode under such force. It happens with TH350's. Their clutch pack design can handle lots of power, but the planetary gear set is the week link. The TH400 trans has additional bracing to aid in dealing with the excessive force transfered from the clutch packs to the gears under high load behind a powerful engine.
I wouldn't trust a stock 4T80E passed 350 lb/ft driving it every day (considering it was driven like I drive my car....HARD!). Anymore than that and I'd consider heavy duty clutch packs to deal with the added force.
As for 40% over stock, that's a maximum torque input of 450lb/ft.....which is a lot, especially for a FWD car who's suspension isn't design to cope with that much torque, let alone what it has from the factory.
The half shafts are a weak point as well. Many 03/04 Cobra owners found themselves snapping half shafts at the track once they upped the power, or in some cases just ran drag radials. The horrendous weight transfer to the rear on our fwd yachts helps ease the stress on the axles, but your still asking for trouble running the kind of power Mark is through the stock units.
As Raze mentioned, the CV joints aren't too fond of excessive torque input either. I bet you could probably have a set of HD half shafts, with beefier CV joints machined for the car as well, but at what cost.
At this point, I've pretty much given up on making the car more powerful, and have decided to focus more on making it more balanced in regards to handling, and managing the power it already has during WOT launches. I feel focusing more on those two aspects then power alone will in the end, make the car much more driver friendly (that is, if your like me and beat the piss out of it almost every day).