If you are looking for the engine bay cover, then you can order a pre-cut mat from NKG (it is not listed on their website but is available if you contact them):
It is a rubberized material and will not break up.
If you are looking for the soundproofing for inside the engine bay, this is no longer available and you will need to make it yourself. NKG mentioned above sells an adhesive soundproofing material with foil that could be cut to fit (different material than the engine cover mentioned above).
The price of the MGFnTFBITZ glass window top is probably the best price around for a new top. The BAS top is few hundred more and even that is priced fairly. Too bad it is only available in black.
The hood in the image is a 'Sportster' hood. It is made by BAS, who were the OEM manufacturers of the original hoods. The Sportster hood was not offered on cars when new but has been available as a replacement. It is a nice looking design but has a small flaw that the glass does not sit as flat as the OEM style. The effect is that the hood does stick up more when folded down. The reason for the difference is the gap between the glass and the bottom of the hood. On the OEM style the gap is slightly larger (i.e. more material between the glass and the bottom of the hood) which allows the glass to sit evenly when folded.
Not sure about the rubbing of frame against the hood. Perhaps this is part of the design of the Sportster hood. The OEM hoods were prone to getting stuck and frame pinching the materials, causing small holes. This was rectified with easily fitted additional straps. These are available from Rimmers.
Sorry, can't help with the carpet fitting. But I did slide some extra carpet underlay under the carpet to help with the carpet pulling out. The result was very successful. I see you can get some flat plastic pieces to help with the carpet issue.
I recently saw these similar plastic pieces as well on eBay. I don't know the seller. Just passing on this information.
Most cars leak from the window cheaters. Putting some extra tubing in both the seals on the door side as well and windscreen sides helps but often still leaks some. As mentioned, no new 'main' seal is available (and I doubt it ever will be). Even if you could get a new main seal, the cheater itself is probably a bit stretched and will catch water (and changing that part is no joke). It was not a good design.
Do you see drops of water on your inner door liner and speaker? If yes, then you have cheater issues. This is also made worse (in my experience) if your car is parked on a slope (facing downhill). It does not seem like much but the small ingress quickly adds up.
The easiest solution (after you have attempted the above) is to put a half cover on car if it sitting outside for longer periods. For shorter periods, I have a couple of small (rectangular shaped) sponges that I place below the cheater on the inside to catch the drops (they rest on the 'ledge') so it does not drip down to the speaker and carpet.
Not so sure about the snorkel. This was a problem on earlier cars but not later ones.
Before pulling everything apart, why not put some paper on your floor the next time it is parked in the rain so you can see where the water is coming in from.
Posting a few photos (of window gaps, water droplets after rain, convertible top condition, etc.) may also be helpful.
You can probably pull back the carpet enough to dry it without having to remove the center console although the seats would need to be removed.
I have a 2004 TF 135. I have retrofitted the dual horns as well as the plastic covers over the engine. The cover on the right hand side sort of contacts with the boot lid bolt and cracks a bit over time. Maybe they are not strictly necessary, but I like them.
In regard to the door post finishers, what exactly is their purpose? Also, if you retrofit them, do you need to drill holes in the post for the rivets that fix them into place? I have seen these types of finishers on other convertibles, so I think they must be more than just cosmetic.
Other 'deleted' items from Project Drive include the front bonnet light, rear boot mesh pocket, wheel arch finishers and owners manual case. There are probably a few more small items as well. I think they also cut some corners when it came to painting / rustproofing, what what I have read.