What version of remapollo you use?
In my A4000D I have 2 behaviours.
On version 1.7
if I use the
If WARN
RemAPollo ....
EndIf
...
It doesn't work, Computer freezes.
On version 1.8 I have to use If WARN.... Or it won't softkick.
In either versions I cannot use DRAP.
According to instructions we have to apply a ptch to 68060.library (60.10), wich I did. (I followed the instructions).
If I use skipromupdate ... it works.
If I use NOROMUPDATE quiet, it doesn't softKick.
Everything works, I understand what you say, I tried it, but maybe I'm still missing something.
From what I see now, only a few parts are rekicked, so, the best solution is to :
a) Make a rom and rekick it by software with your favourite requicker. (but that will still bring you trouble with scsi.device in apollo.
b) Burn ROMs the way you want and simplify S-S by removing manythings.
You already have the most suitable tool installed. I promise you that it won't get any easier with another one 
The main problem is that you have way too much (non standard) stuff going on in your Startup-Sequence, so it's not easy to pinpoint the exact reason for all the issues. I have tried to explain what you can do, but I realize that it may all sound a bit confusing.
So below is hopefully a more simpler explenation of what you can try, which sticks to the most basics of OS3.9 with Boing Bag 2 only (nothing more, nothing less) :
1. Do as I mentioned in another post regarding workbench.library and icon.library. In other words, copy them to the LIBS:OS3.9 dir, and rename or delete the ones in LIBS:
2. Make sure that the C:RemAPollo line looks exactly like this (everything on ONE line):
C:RemAPollo QUIET MAC Modules LIBS:OS3.9/OS_Module1 OS_Module2 OS_Module3 OS_Module4 OS_Module5 OS_Module6 OS_Module7 OS_Module8 OS_Module9 workbench.library icon.library
3. Disable the C:LoadResident and C:LoadModule lines for now by inserting a semi-colon at the beginning of the line (you can deal with these later). The lines should then look like this:
;C:LoadResident >NIL: DEVS:trackdisk.device
;C:LoadModule >NIL: DEVS:battmem.resource DEVS:console.device DEVS:FileSystem.resource DEVS:misc.resource DEVSotgo.resource L:FastFileSystem L:Ram-Handler L:Shell-Seg LIBS:dos.library LIBS:layers.library REVERSE NOREBOOT
4. There is no need for SetPatch to have anything to do with the BB2 ROM updates, since this is already taken care of by RemAPollo. So change this line from:
C:SetPatch SKIPROMUPDATES console.device,dos,filesystem,FileSystem.resource, ram-handler,shell QUIET
to:
C:SetPatch NOROMUPDATE QUIET
5. Save the Startup-Sequence and turn off the Amiga. After a couple of seconds, turn it on again, and now the Amiga should hopefully boot into Workbench.
If the above doesn't work, it may be the result of issues with your 68060.library.
