UPDATE 10-7-15
I obtained another copy of the 3.9 disk. (I assure you I own a real pink copy by the way). I wanted to rule out something amiss with my copy. I also now have the cdrom drive connected to the warpdrive.device instead of the 3000's scsi.device.
I have had complete success through boingbag2.
Here was my procedure.
1) format workbench -clean slate
2) install 3.1 fresh and mount CD0 to get access to the CDdrive.
3) insert new copy of 3.9 disk and create EBD (emergency boot disk)
4) reboot from boot disk
5) re-format workbench -clean slate
6) install 3.9
7) install 3.9 internet software

install 3.9 cdrom driver (to replace the 3.1 driver in DEVS)
9) reboot
10) insert a cd burned on a PC (using windows 10 normal burning) with the boingbag updates (1-4) already decompressed (using winrar).
11) copy boingbag1 folder to RAM:
12) swap CD for new 3.9 disk
13) install boingbag1
14) reboot
15) repeat step #10 through #14 with boingbag2
Everything in the above steps works 100% including using the ROM updates with my warpengine. No problems, no errors, everything good!

Thanks to everyone for the help and education that got to this point. I hope this thread helps others get at least this far in in the future should they run into similar problems.
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I did attempt (and succeed) moving beyond and installing the boingbag3&4 combo (which by the way does not require the 3.9 disk inserted). The install seems to work fine however on restart I get messed up colors on my screen and various commodities return errors on startup. I will continue to try and discern the nature of those problems but I am happy I succeeded through boingbag2 at this point with a stable system.