Each answer is a place, landmark or attraction in Africa, one per country. The answers first traverse all countries on the mainland by crossing land borders, and then the remaining ones go around the continent by sea. Each clue is missing a country name from another clue (not the answer to that clue, just the name of the country).
Notes:
- By request of the Sanity Preservation Institute, some long names have been shortened. For example, if the full place name is "Xyz Royal National Park", the answer will be just "Xyz" (often with "royal national park" or similar as the definition).
- While many of the answers are pretty obscure, all of them are notable enough to have a separate article on the English Wikipedia.
- I have used the same country names here as Wikipedia uses in its article titles. So Eswatini instead of Swaziland, Ivory Coast instead of Côte d'Ivoire etc.
1. Masculine half TV star by wild and unopened [16] waterfall (12)
2. [25]'s leader capable before peak mesa (5 8)
3. Mountain is returning by [43] with no rail signs, twice (6)
4. [50]'s honorific next to violently beat oasis fort (3 9)
5. [49]'s first Shakespeare king leads Shakespeare king's lake resort (4 7)
6. Non-deceased [12] town without town is former capital (11)
7. Grand [4]'s neighbour is ruined city (5 8)
8. Agreed, audiovisual [10] with murderous Bundy's parts forms river mouth (8 5)
9. Dry lake's unconventional US olives draw in [46] couple (10)
10. Chaotic [6] gets a large turn for medium beach (4 4)
11. Ape follows girl alongside [42] capital's leaders to sanctuary (4 2 6)
12. Aged user interface about the case of [54]' capital gorge (7)
13. Get one back inside [45]'s borders leads to capital (6)
14. Forest capital of Neil Young loses ring before [7] finales (7)
15. [14] beginners mischievously zero in to national park (8)
16. Game reserve rampant as a Maria inside [28]'s borders (6 4)
17. [20] capital sides in arbor duck hunt getting rid of hot DC mosque (4'1 5)
18. [17]'s edges both ways with large saline lake (5)
19. Planck moves head back around [15]'s capital, a historic town (4)
20. [9] capital's heart gets a bottomless lake archipelago (6)
21. National park's headless anime holds shelled [8] currency (6)
22. Polyhedrons follow skinned Anubis with [51] capital's heart making ancient tombs (6 8)
23. Latin wife east of [1]'s capital city full of history (5)
24. Losing second chance, [41] lets imp freely to a ruin (6 5)
25. [24]'s top three return after two leading Jews for national park (5)
26. [23] IM gadget conceals city (6)
27. Mind boasts fanatically about brief [19] capital's graves (7 5)
28. Convoluted car band leads part of [36] national park (4 1'6)
29. [48]'s heart in thirds to pot-boil pumpkin tofu leading to ancient city (8)
30. [27]'s leaders go west by hideous double-headed groom's market town (5-5)
31. Heartless fascism crudely follows rest of [26] back to mountain formation (3 6)
32. Soldier holds half of [37]'s headless capital village (5)
33. [13]'s borders hold back Asian people leading to town with waterfalls (5)
34. [47] capital's leader Ben R leaves biosensor to town near canyon (6)
35. Large, leaderless [34] briefly has a national park (6)
36. [44]'s premier duos follow prince of boas oddly to mountain (4 6)
37. Faunal reserve in [32]'s capital (3)
38. Move back and forth behind [2]'s former president leading to monolith (4 4)
39. Gamey endings by inner [35] makes city with palaces (6)
40. [5] capital removes large wing, gets medium capital (4)
41. [18] loses Dench leading to waterfall (4)
42. Wines taken from unorthodox [3] national park (3)
43. Surfing town's actress Julia alongside leaders of [52]'s capital (11)
44. [39] strikes second and third with uneven true mean nail mountain (9)
45. Old Eli returns to get [21]'s initials and extremely habitable islands (4 2 3)
46. [11]'s bottom three follow shelled coral island (6)
47. Lose with abnormal brief [33] inside lake (3 4)
48. [53]' second following reconstructed Baku nature reserve (5)
49. Volcanic village is [31]'s neighbour with strange radical seas (3 3 9)
50. [38] coin with head lost to natural park (3)
51. Natural monument is a venue of the jazzy ABBAs having [30]'s extremities (6 2 3 7)
52. Mountain tribe finally switched sides in coup within [40] capital's borders (2 5)
53. Almost [22] capital second-to-last with inner salad volcano (8)
54. Mixed-up Eve led a [29] natural reserve (6 2 3)
