Sorry, I don't want to be a freaking debbie downer but there are two things I would do different. I would start off with it intercooled, and I would not look down the stroker route.
1)
You are going to limit yourself w/o the intercooler. The T trim could be a great idea for a big build down the road but you will be limited to sub 8-9psi until you intercool it- which defeats the purpose of the t-trim. It is easier in my mind to do all the tubing and setup the first time. I would look into a number of options for intercooling and custom setups. Or talk w/ tank here on the forums, if you want a big build... have you thought about going turbo?
2)
Everything I've read about stroking our 4.6's has been marginal at best. Yes you will have a little more displacement but from what I have heard the gains are marginal. Especially if you are running a t-trim- the power is in adding more psi. Now forging the rods and pistons is a great idea, obviously, but I would keep near stock displacement because the additional displacement doesn't yield much from what I have seen.