Welcome to the forum. Lots of Comet owners here. You didn't have too many specifics on your engine, so I'll just assume at the moment that other than the cam it's pretty much stock. Jay Brown who runs the website here did a lot of FE testing on the effect of different intake manifolds and exhaust manifolds & headers on his engine dyno with different engine combinations a few years ago and published the info in a book, here's a link:
http://www.fepower.net/GFEIC.htmlHopefully Jay will come on here with some advice, but I will say one thing he found was the factory 390 GT exhaust manifolds were very restrictive and not much better than the flat manifolds most other FE's had. One of the first things I would look at would be headers. If you don't intend to hop the car up too much in the future and want to keep it closer to stock you could also consider a pair of the factory 428 CJ exhaust manifolds, they make reproductions too I believe. Whether the 428 CJ manifolds will work for you may depend also on which cylinder heads you have. Headers for a FE are not cheap and there are a few different choices, so you want to pick wisely. You need to consider which cylinder heads you have now, or if you plan to change heads in the future, as exhaust bolt pattern and exhaust port location matters on how well certain headers work and seal and fit. Lots of people here with header experience, I'm sure they will give you advice if you go that way.
One other thing Jay found was the factory "S" cast iron 4V intake manifold also isn't very good for high performance. There were a few different casting numbers, but they all have the letter "S" cast into them. It was ok for what Ford designed it for, low end torque on a stock street car, but there is room for improvement there too. There are a few good choices of intakes you could swap too and gain some power ( and a few bad choices ), again it will depend on how far you intend to go as to which ones are the best choice.
The distributor and ignition system are probably the other place to look at first. After 50 years many FE's no longer have their original distributor. Check the I.D. number stamped on your distributor to see if it is still original, then you will want to check what the initial ( idle ) and total timing are and at what rpm the distributor stops advancing. Before going too far with modifying the stock point distributor you will also want to decide if you want to change to an electronic ignition, and which one. Again, lots of people here to give advice and experience. Some of your choices on electronic ignition are: a Pertronix conversion, a Ford Duraspark magnetic trigger distributor and either a Ford Duraspark box, or some aftermarket box like a MSD, or a MSD distributor with a MSD box. There are others too.
The factory Ford Holley 390 GT carb is a good one and will work fine if in good condition, at least until the point you step up the power enough that you need a bigger carb.
Tell the gang here what you have and what you want to do and I'm sure you'll get steered in the right direction. Post up some pictures if you've got them. Good luck.