Focus on what you want to build power wise. This is what I would suggest if you are going to maximize your combo but again you need to have a goal and build around that goal. To me the cam is the brains of the operation and it basically tells the other parts what to do. Those parts need to be sufficient to support what the cam is trying to do.
Lets just get this out of the way, the heads you have will kill a N/A 331 or 347 as they were never meant to move that much air. My suggestion would be to start stock piling the parts to build what you want while you are driving the car which means finding the block that you will build the motor with.
Induction
You will want a good air filter than can flow enough air for what you are building. You can figure the maximum air flow rate and then visit air filter websites and they typically list the flow rate of a given filter. I would suggest a minimum of an 80mm mass air meter (if you stay mass air) and a minimum of a good (read Acufab) throttle body. Piping diameter from the filter to the throttle body will need to be a minimum of 3.5" with some fittings and good clamps. The upper and lower intakes would need to be sent to TMoss for some work. Again, I am going to suggest the AFR Renegade heads as bang for the buck they are pretty damn good. You will need rocker arms and I am a fan of Scorpion and Harland Sharp bu there are others, IMO you would want a custom grind cam but you can definitely work with Comp Cams or the like and see if one of their off the shelf cams will get you where you want to be. You will most likely need push rods but those are figured out when assembling the motor.
Short Block
I would not recommend more than 11:1 on pump gas. Realize that a stock roller block is on average good for 500 fwhp before the mains start walking around which is what mostly kills them. A main girdle will not stop this but below this level they seem to help. I said seem as there is all kinds of back an forth on this but I do have one on both cars. Get a good rotating assembly like Scat, Eagle, Coast High Performance with flat top pistons that have reliefs that will clear a minimum of 2.05 intake valves, There are other manufacturers of rotating assemblies but I just grabbed the ones I am familiar with. Get a good harmonic balancer like a Romac, Fluiddamper, FMS, etc. and for the imbalance of the rotating assembly (most likely 28 oz). Ring packs are another topic of debate and some others on here can probably recommend some as I just go with what my engine builder tells me. Get a good oil pump and you do not want a high volume one as there is no need. My engine builder works them over and sets the pressure output. Get an ARP oil pump shaft as its cheap insurance. Stud the mains, heads, rockers, valve covers and intakes. Rods should come with good fasteners so no worries there. If you run a main girdle the main caps typically have to be machined and you have to get main girdle specific studs.
Exhaust
Headers are another topic of varying opinions but long tubes will build more power. Their down side is head soaking the starter (there are ways around that) and just in general being a pain to install and remove. Slip tube style help with this but they will have small leaks at the collector. 2.5" is a minimum and really 3" will make a difference. At some point I will be moving to 3" but I have been putting it off as it will take custom tail pipes to get around the torque arm and
panhard bar. My buddy 86 with a 408 picked up three tenths at the track going from 3" to 4" from the Cooks headers to the turn downs. That is a lot more motor than you are wanting to build but its a good example of exhaust restriction.
Fuel System
I would say a minimum of a 255 lph pump and ditch the stock lines between the hanger to the fuel rails. This is just me and I am sure others will chime in on how they are making in excess of 500 rwhp on all the stock stuff. My experience has been different so do some research and by all means listen to others that have the real world experience as well as there is more than one way to do this.
Ignition
Stock distributor will work fine and probably one of the best out there when staying with the stock ECU. You should also look at good plug wires and again lots of opinions out there. I run the Motorsport 9mm wires and they work great for me but lots of options. Run a good plug like an Autolite and in the correct heat range. The stock ignition is pretty good but I run MSD boxes and again opions will vary. Aftermarket ECU's, Crank triggers and such are another level and at that point you maight as well go coil over plug or COP but hold on to your wallet. That can be something you do after you get it running and want to self tune.
Tuning
Stock ECU means you will need a chip and I would recommend a dyno tune. Aftermarket ECU's are getting more and more user friendly but if you do not understand all that stuff find someone that does and have them teach you. The stock ECU's are like a mid 90's computer processor wise versus the new ECU's which are a super computer compared to the stock stuff so you can do a lot more with them.
Drive Line
You are going to need a good SFI flywheel and a good clutch set if which both will be needed to balance the rotating assembly. The life span of your T5 behind this much hp with good tires could be a day or years. I would sell it and get a T56 or TKX. This will suck money wise but it won't break either. I will eventually head down the T56 route but that's a different story. Get a good drive shaft i.e. stock DS balanced and new u-joints at a minimum. Adjustable
control arms so Maximum Motorsports. Good springs and dampers will make the
control arms work even better.
Remember, a motor is just a big air pump so you have to get the air in and get it out and have enough fuel to burn and a good spark to light it off. From ther you have to get it to the ground unless you just want to impress everyone with smokey burunouts but I will say I am fan of a good version of a John Force burn out.
I am pretty sure I have wasted enough of your time with all of this but I will say again that you need to listen to some of the guys on here as they have waaaay more experience than I do. Can you build a 331 or 347 with the GT40 heads? You sure can but you will make GT40 head power so again have a plan and build to it.
This is just a hobby for me so if I blow something up then the car sits, I cry over dead presidents, drink a few beverages and then figure out how I am going to get it running again i.e. rob a bank.