I used different media, combined with the proper CHS settings in HDToolbox I got OS3.9 working on the 64GB SSD, as well I can now copy large files (400MB to the SSD) with no problems. I have a few quirks and things to do remaining.
Hitting RAmiga-E to bring up the "Execute" requester causes the system to crash. This actually happens with the original load of the OS which came with the computer. Mind, it was probably loaded from the same good media.
I'm going to work to identify the BoingBag level tomorrow to see what needs to be installed. I am pretty sure it's an original release of OS3.9 considering the "AmigaOS ROM Update" is v44.26, but what I found interesting is the bad media gives me the installation option of installing over 3.0, while the good media installs over 3.0/3.1. Maybe it is a BB1 media?
So far everything is working well. Using
hddreport to get the proper settings for HDToolbox seems to have fixed the problem of moving large amounts of data over to the SSD. (Yes, for the n-tieth time I did check MaxTransfer at ever load.)
At this point I have MUI3.8 and Poseidon installed (RapidRoad on X-Surf 100.) Oh, and FBlit and FText. Tomorrow if I have time I will install Roadshow and DOpus and try out some WHDLoad games (currently extracting from USB.) Probably wouldn't hurt to update some MUI classes and install WarpDT datatypes. I'm using an Indivision AGA MKII and once everything else is stable I'll install my new VA2000.
I think I need a "fresh load" FAQ to help me sort additional enhancements I should install. I remember a while ago I posed a question about that, I'll try to dig that up.
One nasty little thing niggling me is my 3640 is a Rev 0. Haven't decided if I should do anything about that (other than regret ever selling my WarpEngine 4040.)
Thanks to all. It looks like my original problem is resolved!