Mr. Taylor,
I am on a break right now, so response time is to your post is limited. As for the Peace River, as I said I have only dove it a few times, which is ironic, as my mother's family history in the Arcadia (Pine Level) area dates back in excess of 200years--which means, over the years, I have spent a lot of time in the area. However, with 10 aunts and uncles, most trips have been too family oriented for me to get away for any length of time.
Your synopsis of the river above pretty much sums it up. River condition (primarily) determines whether you use scuba, snorkel or just wade and dig. If you plan a trip to the Peace, the guides you have been made aware of should be able to advise you on conditions you could expect--which will dictate what equipment will be appropriate for the water level.
I have never been there when the visibility was more than minimal--but based on your posts and SC rivers experience that should pose no problem.
I have dove the Suwannee hundreds of times, mostly between the Branford area and Fowler Bluff. These days, due to a drawn out retirement move, I haven't been in the Suwannee since late last year. Back when making frequent dives, I would dive when I could, anytime during the year (depending on river level). But I concentrated my dives to the winter months until the late winter/spring rains caused flooding. I preferred the winter for several reasons. During the winter, generally the drier season, the river is lower, as little water from the Okeefenokee feeds it. This means, especially in the lower river, most of its' volume is from the many springs (and the Santa Fe River). As a result, the water is as clear as can ever be expected, and the spring water moderates the temperature--I have dove it quite a few times in a 3 mm suit. Another plus is, with the exception of a few "old timers" fishing, the jet ski morons grace us with their absence, and the people with badges are generally in a coffee shop in Chiefland instead of being on the river.
One last point you mentioned, before I have to get back to work (my retirement is still pending to as late as the end of the year). What type boat to use---any boat that is good for diving, assuming you aren't using a 30 footer--which would probably draw too much water for many areas of the river, especially in the upper reaches, but in the lower part a bigger boat would probably be ok unless the river is really low. I believe the house boat rentals available at the mouth of the river limit the up river travel to Branford. I and my fellow divers boats, over the years, have ranged from 12foot Jon-boats, to 18 or 19 footers of several different styles.
I prefer a 15 or 16 foot mostly open type boat. Our usual "suiting-up" procedure is to beach our boat along the shore, put on our gear and take the boat off from shore and anchor it in line with the area we will be diving from shore. We then work up river (or closer to the Gulf--up current). When done we just drift back to the boat and push it back to shore to shed our gear.
Though there may be a guide(s) that work the Suwannee, I have never heard of any, and since I never avail myself to guides anywhere I dive, I would be one of the last to know of any. As for where to put in---the short answer is wherever you find a boat ramp!! The Suwannee is "blessed" with many ramps. The best place for location is a Florida Gazateer, which in addition to showing more ramps than a regular FL map, it shows roads in much more detail. Which is useful as some of the ramps are in remote areas---just try and find the ramp at the old Wannee steamboat landing without some help!!