I'd first like to start off with a congrats on your interior, it will be the hardest part of everything, atleast in my point of view
Well this sorta seems like a dream build... So i'll tell you what i'd go with, after viewing all the topics in tech/talk for the last 7 months.
Engine:
Pro-m or C&L 75-80mm MAF
BBK fenderwell CAI
Edlebrock 65mm TB and 65MM EGR Spacer
Cobra intake replica ported by Tmoss
255LPH Walbro fuel pump
AFPR (any brand)
24LB/H Ford injectors
Ford valve covers
AFR 185 heads
1.72 roller rockers
hardened pushrods
Stock cam
Canton oil pan
FRPP ceramic coated shorty unequal length headers 1 5/8" primarys, 2.5"
BBK o/r H pipe 2.5" (Or catted pipe)
dynomax race bullet or spintech mufflers 2.5"
any set of 2.5" tailpipes
MSD dizzy and coil
Hardened oil pump drive
Power Master one wire alt.
Battery relocate kit
Alum radiator off Ebay, direct Mustang fit (Less than $250)
Under drive pulleys with a alt. overdrive.
Remove the A/C, power steering, and smog pump (Wait, your in Cali aren't you?, never mind) and go with a idle pulley for the a/c and a manual rack and pinion from AutoZone.
get a $700 shortblock off ebay with a oil pump and a gasket set. Then get a double roller timing chain, water pump, and any other misc. rebuild items you would need.
Then get a 50oz. balanceer (stock style is fine) with a light weight 50oz. flexplate, custom torque converter, manual valvebody, shift kit, shifter, alum driveshaft (can be had out of mini vans for large savings, do a search) and 4.10 gears, 31 spline spool, 31 spline 5 lug star cut axles, rear end rebuild, and any other misc. items.
I think everyone else has taken car of good choices for
suspension and brakes, but please don't extend your fenders
One last note, hiding the wires, and welding all the holes up, smoothing out the engine bay, and polishing all the misc. parts (like alt, belt tensionor, intake, misc.) would look GREAT, and would make it that much easier to get into a mag!