FireWire frustration

Question

I bought an iBook 600MHz 14-in locally. (Be warned that this anecdotal intro. may having nothing to do with the main matter.) The seller stated that the Li-Ion batt. had been kaput for two years. Sure 'nuff, the battery toiled not, neither did it spin. Backup battery was also feeling poorly. (So would you after two years in a cupboard, but after a week on the AC adapter the iBook can hold date and time briefly when it is off the adapter.)
The iBook started up from its AC adapter, but kept freezing at the menu-bar with a snivel about wrong date and time. No big deal. Get hold of it in target disk mode from my wife's eMac 1GHz and give it the thrice-over.
Rescue of the iBook was straightforward, by way of a complete wipe of the stock 20GB HDD (>85% filled with former owner's files, which I archived in case she wanted them, which proved not to be so), partitioned into nominal 2GB (OS 9.2.2) and 18GB (OS 10.3.9 fully updated as far as SecUpdate 2007-007). This to-ing and fro-ing included much plugging and unplugging of FireWire and ethernet, but always with both Macs and a LaCie d2 external HDD quiescent at the times of disconnection. The only bugbear in the process was DiskWarrior's observation that the iBook was so RAM-deficient (stock 256MB) that it would take longer than usual for its work, and it did.
Now the story gets interstin' and to the point. Next evening was Retrospect time for the eMac, but it could not see (on the desktop or in ASP) the target LaCie d2 as it had done weekly for the last year. Testing by substitution cleared the cables and the d2 of fault. Oh, oh! Fried FireWire ports, anyone? Very tasty when they are part of the logic board. Sheesh. A week later I used USB instead of FireWire for the backup. Max. transfer rate was reported by Retrospect as <40MB/min (instead of up to 600 normally with FireWire), and I stopped the process at 5hr. Then came a thought. What if the death of the FireWire ports was software- rather than hardware-related? I booted the eMac from a second 10.3.9 partition of its 80GB HDD, which I blessed myself for having had the forethought to create when I set up the eMac a year ago. eMac saw and mounted the d2 LaCie's three volumes.
So the question is, what software restoration to the main 10.3.9 partition can restore its FireWire functionality? PRAM reset? Re-installation (shudder) of 10.3.9? Any ideas, please?
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Answer 1

Clearly enough, the eMac, and equally clearly, FireWire as a networking and peripheral-connecting tool. The iBook, however, as the only different factor in the relationship between the eMac and its backup LaCie d2 external drive, may have been the precipitating cause, and thence the reason for its mention. The iBook certainly left traces of its connection to the d2 by renaming the d2's boot volume with its own name in the Sharing CP.
I should prefer to understand the defect and its remedy before I undertake the blunderbuss approach of an archive-and-install, despite that the puzzle appears to be software- rather than hardware-related, as is evidenced by the normal mounting of the d2's volumes when a different partition of the eMac's HDD is used as startup volume. Insofar as DiskWarrior 3.0.2 showed this morning that the affected volume of the eMac had 19% fragmentation of its file directory, I may have to excuse the iBook from the investigation. Such magnitude of directory fragmentation is beyond my experience under any circumstance but a fresh System installation of a Classic OS, which often reaches 30-40%. The cause of the fragmentation may more probably be three power outages within days a few weeks ago, but the effect was not seen in three iMac 500s that also went down at the time. However, directory defragmentation did not restore the eMac's sight of the d2 external drive, and neither did the four-fingered salute command-option-p-r.
The copious references returned by a Google search with 'FireWire port failure' are inconclusive and unilluminating. They mention PRAM-zapping, and they assign much blame to supposedly shoddy construction of ports and cables without citing meaningful specifics. However, this instance does not appear to be a hardware fault, and I do not use any but first-quality short shielded cables. I should be interested to read about core system services that could be implicated in the failure of FireWire ports.
de