Re: what pickup should i use in the middle?!?
Eblis,
Im very picky about hum and my main rig is not hum friendly. I have a JB in the bridge, not a JB jr. The guitar is completely hum cancelling. I also have a series/parallel switch on the guitar so that I can thin out the JB when combined with the Hot Stack. It makes for a more realistic #4 position, though the JB full on with the Hot Stack also sounds very nice.
The JB jr and 2 Vintage Rails will make for a very cool Strat, no doubt about it. Going with the Cool Rails or lil59s is also a cool way to go if you want a thicker and louder tone from the mid and neck pickups. I've tried a few different combinations in my Strat (Hot Live Wires, 3 Hot Stacks, 3 lil59s, CC + 2 lil59s, Custom + 2 lil59s, C-5 + 2 lil59s, JB + 2 lil59s) and the JB/Hot Stack/lil59 is by far my favorite so far. The series/parallel and bridge pickup on/off switch with those 3 pickups give me quite a few very useable tones from metal to blues.
Stonabus,
There are an endless variety of combinations that can work. I don't normally put a hotter pickup in the mid positions of Strats, but that doesn't mean you couldn't. The HR/CR/Lipstick combo might be very cool depending on what you wanted from that guitar. There is no reason to not put the lipstick in the middle, other than you may run into balance issues and the Lipstick pickup may get a bit overpowered, especially by the HR. That doesn't mean you won't like the tone though.
It is generally recommended to use neck model pickups in the mid positions of Strats.