It depends on what all you're doing.
An engine can be anywhere from free on up to as expensive as you want it to be (heck, if you want you can blow a hundred thousand on one like they do for the 358cid Windsors they use in Nascar), the parts that go on it are the same, stock exhaust manifolds start at $50 for rusted but usable pairs on Ebay and mass-produced headers go up to about $1000, custom-built headers will cost even more than that. Exhaust systems start out at $200 or so for an independent shop to put 2" pipes and glasspacks under it and the sky is the limit from there, Bassani, Borla and a few others have mufflers that cost a few hundred dollars, Flowmaster mufflers start at about $50 each, glasspacks are as cheap as $15...
You're asking a pretty open-ended question here... This is what I have tied into mine, but remember I do ALL of my own work so my labor is free:
Engine: 302 roller cam shortblock from a Crown Vic $100
Heads: Ported E7TE "5.0HO" heads FREE! (traded some work for them)
Intake: Weiand Stealth $180
Headers: Dynomax Blackjack $140 (and these were used, they're not made anymore)
Carburetor: Edelbrock 1406 (600cfm, Electric Choke) $275
Distributor: FoMoCo points-type distributor with Pertronix module $150
Plugs: NGK V-Power $18
Plug Wires: Accel Spiral Core 8mm $50
Valvecovers: Chrome Ford Racing $25 (used)
Motor Mounts: Stock Mustang II $178 (used, good luck finding these if you need them and don't have them).
Water Outlet: Chrome Mr. Gasket $10
Radiator: '68 Mustang 289 replacement from Ready-Rad $150
Air Cleaner: Chrome Edelbrock 10" $30
Cam: Ford Racing B303 $200
Transmission: TBD
Starter: TBD
Clutch: TBD
Flywheel: TBD
Fuel Pump: TBD
Timing Cover: Stock Mustang II (currently bidding on Ebay for it)
Subframe Connectors: Stumpy's $92 (gotta catch a set on Ebay, but I know how much he charges for his "Buy it now" price)
Exhaust: Hooker Aerochamber Mufflers on 2.5" pipes about $300
Notice I haven't even decided what
tranny, flywheel, clutch, starter, or fuel pump I'm going to run yet. Those are costs that will have to be factored in, right now I'm leaning toward going with a C6 automatic (lot of work on the tunnel with a sledgehammer!!!) as my left knee currently couldn't take pushing the pedal on a decent clutch anyway and I want the durability for the future when I get AFR 185 heads, a Holley 670cfm carburetor, and possibly nitrous in the car.
Taken to a shop, the labor alone to screw all of that together and get it running right would run you about $2000...