1. A 6-speed won't fit into the 2.7L without some huge modification.
2. When it comes to headers, you should probably head to LC Engineering to find some there.
3. Popular lifts include ReadyLift's and FatBob's. FatBob's are a tad cheaper than Readylift's.
Readylift's here: http://www.readylift.com/c-107-toyot...-275f175r.aspx
4. You can run 18" wheels but as for tire wise, I would have to look that up later on. But maybe someone can chime in and help you.
5. I personally don't do a intake system because there is very low performance gains and only at higher RPM's, unless you drive like that. The stock intake will be good enough for most people. I popped in a AFE performance filter and I notice a difference only because I drive 75+/2500RPM+.
EDIT: Also welcome to TW haha
EDIT 2: You can probably run max 225/60/18 if they make them lol but you're better off lifting it first because that opens up a bunch of tire sizes. You can use the TacomaWorld Tire Calculator to punch out the numbers yourself: tire size calculator