Do you have all your drives connected to CSPPC's SCSI? Could it be that your Amiga is looking for harddrive connected to motherboard? This happens with A4k, but that has IDE so I'm not sure about this. Maybe creating custom rom with RomSplit&Remus and removing the A3k's own scsi.device completely speeds up things.
As to your mouse pointer - are you using some kind of mouse adapter? Sometimes they get jumpy, especially after running some programs/games in different resolutions (warp3d games etc) and then coming back to workbench. Try normal amigamouse without adapters and check if this is the case, just remember to comment drivers for your mouseadapter out first.
-q
