Thanks for all the feedback on the Clam, folks.
Was trying a few things last night and - whilst there are alternatives to achieving a similar thing (e.g. time-limited fortress shield, flux shunts and no fortress shield) I don't actually feel they do anything that's going to change the balance sufficiently unless I completely change the character of the ship - and in that case I may as well just get rid of it or call it something else.
Reducing flux characteristics slightly wouldn't harm, perhaps.
The Clam is supposed to be an escort - a valuable, hard-to-kill escort that can soak up fire and let off a few Pilums. It's not, in truth, supposed to appear in fleets in any great number - which I think is the main problem (due to the frigate line-up - they are one of the most common ships in the JP fleet).
Whilst they are live, in a fleet arrangement - they should be an annoyance. Whilst on their own - they should be easy to pick off. Both these are true (survivability is great, but mobility is dreadful). Arguably Clams are less frustrating to deal with than Phase Ships, and in some respects they behave more fairly - unless, I guess, they appear in significant numbers.
I think a better solution would be to keep the Clam pretty much as it is, greatly decrease the availability of the Clam (treat is as a high-performing Elite ship, like the monitor or Phase ships) and introduce a couple of other frigates to fill in different combat-oriented roles around the gap left.
Notably vanilla throws up some fleet combinations that are equally as infuriating without specific hard-counters - Herons with helmsmanship officers backed by a fighter force; Phase fleets; Monitors with the right officers - many others I'm sure - so I don't think it's worth overthinking the fact that they are annoying and I want to at least maintain some clear diversity in the ship roles.