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diver - 1 across is definitely totally thematic. I made a guess which proved correct.

That was brutal for this solver. I was convinced that I had a pattern for encryption - but not so.

numbskull, thanks for your confirmation about the thematic in row 10. I'd have solved it ages ago if I hadn't made a stupid error entering 22d into the grid. Now that I've spotted my mistake and corrected it, everything else has fallen into place and I've finished the puzzle - at least 12 hours later than I might otherwise have done!

Thanks to all for their help, especially Merenz. I lost several hours through having used S in 3D rather than Z! I should have been more concerned about the lack of parsing with the S.

I took it from the opening words of the preamble that what you enter in the final grid are the thematic items, not the gibberish encoded versions. This shows that you have properly identified said items - and the grid looks a lot prettier! BTW, what letter is missing from 28d ?

I’ve kept them as they are Marbles as it doesn’t specifically say to decode them.

Getting the code right is only possible if you have the right items anyway due to the jumbled down entries.

marbles,
it is 7 letters , and goes after the entry. ends in N.

a micron-sized particle that contains mostly triglycerides with some protein

Thanks to everyone here, and to my amazement, I’ve finished it. Would have given up long ago without this forum.

Rad, I think I have given up despite all the forum help!

Thanks Sunray, I had a blind spot re the longer 'letters'.

Dsc, I think there is no shame in giving up! I couldn’t believe it when I read the preamble and saw that several long entries were not only unclued but also encoded, while some other entries intersecting those unclued entries were jumbles! A denial of all the things that make solving crosswords an enjoyable and satisfying experience. On the other hand I must admit that solving those down clues with missing ‘letters’ was worth the (not inconsiderable) effort.