As far as a sub goes, can I offer up an easy solution...? Like you, I was going to build something into the original hole, but it's really only a 6" hole, and the space behind is an awkward shape.
Instead I bought a Fusion 8" active slimline sub (relatively cheap in NZ because it's an NZ brand, it is available in England and is probably £150 in your money). I screwed this onto the front of the bulkhead behind the driver's seat - on top of the carpet, which kills any rattles. Built-in amplifier, good solid kick to it. The enclosure is hardly noticeable with the seat back in the usual place - fits nicely.
You really don't want to be mounting a real sub inside that cubbyhole, as there are lots of things to rattle in there
Mounting on the outside causes no difficulty at all - easy to get the power to it (battery is right behind), easy to run an RCA cable through the centre console and out under the back (there's foam underneath the carpet).
As for the front speakers - I do prefer sticking with the 5x7 size, but Infinity Kappas were larger (6x8) and a real nuisance to fit. The tweeters were much larger too. I fitted these to my last Spider, but in my current Spider I've still got the originals. Sound OK really, it's hard to justify trying to improve them - the biggest issue with the front speakers is a difficulty in getting any acoustic sealing. The shape of the hole in the door trim is quite unbelievable - there are a series of steps and the speaker has to come out to reach the bolts that hold the door trim on. If you fit a 5" round speaker, again there will be no acoustic sealing unless you do something very clever. Even the clips for the grille seem designed to require large slots in just the wrong places. The original speakers attempt to seal onto the grille, not into the door.
So, how about an 8" active sub, a new head unit, and then see what you think about the original speakers?