I'm at the same point you are. Recently bought a bone stock 90 with 46k miles. I also want to start tearing into the motor but think I am either going to leave it stock or wait until I do the H/C/I swap all at once.
Here's my 2 cents. I wouldn't waste the time or money swapping out the intake or putting on a 70mm TB (which is too big for your setup) until you put a better set of heads on it. It is true an aftermarket intake will flow better, but the restrictive heads will certainly limit any HP gains . The 70mm TB won't give you any more HP than a 65MM on a stock motor. You also want the MAF to be at least as big as the TB.
Trust me, once you change the intake it will only be a matter of time before you want to swap heads, then you will have to do it all over again. Rather than gain 10-15 hp from the intake/TB swap, you may want to wait to get a 70hp bump from the H/C/I swap. That should put you around 260-275 rwhp.
If you still want to go with the intake, first determine what you want to do with the car- DD, weekend warrior? Do you want it N/A or power adder. That will dictate what intake to go with. For a cheap n/a DD, it's hard to beat a TMOSS ported Explorer GT40/cobra intake. I've used the Ebrock Performer. The Performer II is a better choice if you go with a supercharger as the rpm range is higher. The TFS intakes are also a good piece. They make 2 one for lower and higher rpm.
I've been playing with mustangs for over 30 years. Once you start modifying the car, it won't stop. Make a plan, a budget, and choose the right components. I've seen many people spend a ton of money on mismatched parts and wonder why their car runs like crap.