I've heard that prolonged soaking in vinegar leads to the metal pitting. That's why I go for a quick soak and scrub. Maybe I've heard wrong?
The wood is definitely a challenge. Although getting the rusted bolts loose was a hurdle, doing it without damaging the wood was really hard. And the part under the metal sleeve at the end was damaged bad. A real jigsaw puzzle to glue back together. But it turned out good.
Vinegar is an acid and if you leave it long enough, it will begin to eat the base metal. You also need to thoroughly rinse after taking it out of the vinegar, then protect with either oil or wax. I have seen no ill effects on steel from doing a vinegar soak, but I do check things at least once a day to scrub off the rust(stainless steel wire brush) that has come loose, but not dissolved or fallen off yet. Once all the rust is gone, I pull it out, rinse, and oil. I've got some really crusty tools to clean up, and they will probably have to soak several days. Soaking also seems to be somewhat temperature dependent, works slower when it's cool, which seems to be the forecast here for a few days.
I used a product called Evaporust(harbor freight and I think orielly's carry it) on some tools and such a while back. It absolutely will not harm the base metal, and rust literally falls off after soaking in it a while. The downside to it is the cost. It's around $23 a gallon and while it can be strained and reused, it eventually loses it's effectiveness. It gets pretty expensive if you need much of it. There are other similar products out there but I haven't used them so I can't comment on how well they work.
I've also used electrolysis and it works quite well. It does have it's quirks though. Museums use it to restore metal artifacts because if done correctly, it doesn't harm the base metal either. Super easy and cheap to set up and you can go as big or as small as you need.
PB blaster is about the best over the counter penetrant I've used other than Kroil. A 50/50 mix of acetone and ATF works as well or better than kroil. The acetone/ATF won't stay in suspension though, so it's best to only mix what you need at the time.