The sentence is brilliantly constructed to reflect the confusion of the Athenian rout – Thucydides at his most vivid.
ἄλλος ἄλλῃ is dangling without a verb of its own, but conveys as a sort of adverb to what follows the disorganized scatter of the ships.
But I think the sentence as a whole is not too difficult because the elements are clearly articulated.
The overall contrast: ὁ μὲν ναυτικὸς στρατὸς is balanced by ὁ δὲ πεζὸς. The subjects of the two balanced clauses are singular, but the verbal elements shift naturally into the plural:
The naval forces, ὁ μὲν ναυτικὸς στρατὸς ἄλλος ἄλλῃ, ὅσοι μὴ μετέωροι ἑάλωσαν, κατενεχθέντες ἐξέπεσον. . . This itself is articulated into a sort of μὲν δὲ contrast without actually being framed as yet another μὲν δὲ, which might seem excessive: some crews μὲν were captured at sea; others δὲ were forced to the land and were cast onto the shore.
The ground forces, ὁ δὲ πεζὸς οὐκέτι διαφόρως, ἀλλ᾽ ἀπὸ μιᾶς ὁρμῆς οἰμωγῇ τε καὶ στόνῳ πάντες δυσανασχετοῦντες τὰ γιγνόμενα, are then broken into three groups in a sort of tricolon abundans:
- οἱ μὲν ἐπὶ τὰς ναῦς παρεβοήθουν
- οἱ δὲ πρὸς τὸ λοιπὸν τοῦ τείχους ἐς φυλακήν [παρεβοήθουν or some such verb]
- ἄλλοι δὲ καὶ οἱ πλεῖστοι ἤδη περὶ σφᾶς αὐτοὺς καὶ ὅπῃ σωθήσονται διεσκόπουν.
The key to reading a sentence like this is simply to take each element into which the sentence breaks down as it comes. The logical structure:
τότε δὲ ὁ μὲν ναυτικὸς στρατὸς ἄλλος ἄλλῃ,
- ὅσοι μὴ μετέωροι ἑάλωσαν,
- κατενεχθέντες ἐξέπεσον ἐς τὸ στρατόπεδον
ὁ δὲ πεζὸς οὐκέτι διαφόρως, ἀλλ᾽ ἀπὸ μιᾶς ὁρμῆς οἰμωγῇ τε καὶ στόνῳ πάντες δυσανασχετοῦντες τὰ γιγνόμενα,
- οἱ μὲν ἐπὶ τὰς ναῦς παρεβοήθουν
- οἱ δὲ πρὸς τὸ λοιπὸν τοῦ τείχους ἐς φυλακήν,
- ἄλλοι δὲ καὶ οἱ πλεῖστοι ἤδη περὶ σφᾶς αὐτοὺς καὶ ὅπῃ σωθήσονται διεσκόπουν.
I think the two difficulties are οὐκέτι διαφόρως, and, as you noted, πρὸς τὸ λοιπὸν τοῦ τείχους ἐς φυλακήν.
οὐκέτι διαφόρως looks back to the differing reactions described in section 3:
εἰ μέν τινες ἴδοιέν πῃ τοὺς σφετέρους ἐπικρατοῦντας, ἀνεθάρσησάν τε ἂν καὶ πρὸς ἀνάκλησιν θεῶν μὴ στερῆσαι σφᾶς τῆς σωτηρίας ἐτρέποντο, οἱ δ᾽ ἐπὶ τὸ ἡσσώμενον βλέψαντες ὀλοφυρμῷ τε ἅμα μετὰ βοῆς ἐχρῶντο καὶ ἀπὸ τῶν δρωμένων τῆς ὄψεως καὶ τὴν γνώμην μᾶλλον τῶν ἐν τῷ ἔργῳ ἐδουλοῦντο: ἄλλοι δὲ καὶ πρὸς ἀντίπαλόν τι τῆς ναυμαχίας ἀπιδόντες, διὰ τὸ ἀκρίτως ξυνεχὲς τῆς ἁμίλλης καὶ τοῖς σώμασιν αὐτοῖς ἴσα τῇ δόξῃ περιδεῶς ξυναπονεύοντες ἐν τοῖς χαλεπώτατα διῆγον
πρὸς τὸ λοιπὸν τοῦ τείχους ἐς φυλακήν – here you have to remember that Athenians abandoned the upper part of the wall in 60.2.
ἐς φυλακήν[παρεβοήθουν] – maybe “they ran to what was left of the wall [and grouped] into a defensive posture/formation”.
Sight-reading Thucydides without any commentary or other aids requires a knowledge of Greek that I don’t have. But I take comfort from Dionysius of Halicarnassus, who observed that the Greeks of his day (the Augustan era) needed help understanding Thucydides.