[Three Peaks]

I guess I'm in the camp of trying to enjoy the car as is without too much expenditure if you plan on getting most of your money back out of the car later.
The 351C should be plenty of engine for the car if it is set up right. Change the tranny and pedal box and you're home free. IMHO, the 5 speed is the way to go.
The most painless way to go would be to collect parts over time as you see good deals come up on the classifieds, ebay, craigslist, etc... and store the parts until you have everything you need. You'll be amazed at the money you can save by buying parts this way.
I would go with a hydraulic pedal box set up like the Wilwood unit and a hydraulic clutch slave cylinder.
Keep you eyes open and you should be able to pick up a clutch new or with very few miles on it for around $200 including pressure plate, throwout bearing, etc...
Blowproof bellhousing for a Tremec is going to run $200 used, $375 or so new.
Hydraulic pedal box with master cylinders and remote reservoirs will run in the $300-400 range for Wilwood units.
You'll need an aftermarket shifter and they'll run $125-200 depending on the unit.
Watch the classifieds or craiglist and you can find a Tremec 3550, 500, or 600 for around $800 used in good condition.
You'll probably need to have a new driveline built also so figure around $200 for that unit.

So, on the low end you're going to be into it around $1800 minimum if you're a good shopper- plus installation unless you can do it yourself. Not a bad deal really for what you would gain in the deal.

Contemporarys are very nice replicas and worth spending a bit of money on to get it like you want. If you would like to keep it, don't worry how much you spend on it as long as you are doing it for yourself and you enjoy the car. Not many Cobra replicas on the market as solid feeling as a Contemporary, IMHO.