Everyone has their opinions so here's mine. At 113k miles changing your flywheel IMO is a good idea but if you drive mostly on the street I would avoid a light weight flywheel specially with the clutch you chose. It's not a long life clutch with it's limited friction surface area. It's a good clutch that has its place but the street with stop and go traffic isn't it. Add a light weight flywheel and you sacrifice the inertia of a stock flywheel and the problems of using this clutch on the street are amplified. Taking off is going to require a higher rev then what you are now use to and it's going to shorten the life of the clutch even more.
For the headers it's 6 of one and half a dozen for the other. The trans being out may help but they could also get in the way of putting the trans back in. Again though, if you are driving mostly on the street I would suggest shorty's. They don't scavenge as well but they work better with the O2 sensors so they create less problems with tuning. This is assuming you are going to keep your car legal.
Just some things to consider.