Stock, pre-gapped plugs. Indexing is just lining them up so they face the intake valves.
FORDMUSCLE.com web-magazine - How To Index Spark Plugs
I haven't needed them but here's something if you run into trouble
ACCEL Spark Plug Indexing Washers - SummitRacing.com
For the throttle body bypass, you loop the coolant lines that go the the TB together. You can either use something to connect them or just replace them with one section of hose. Look under your TB and find the hoses that face toward the ground, trace them back to the coolant neck - these are the hoses you'd connect together. Google can explain how and why better than I can.