How Much RAM is installed? If not 4MB, you need to max it out. You're already running on a hard drive. So that's about all you can do on an SE without adding an accelerator, which at that point you are better off upgrading to an SE/30. It is possible that adding a dedicated video card to the PDS slot and external monitor might improve performance, but they are hard to come by, and I think the bigger problem is not rendering the video as much as it is trying to pump out a lot of real time MIDI data via an 8MHz 68000 CPU off a slow disk drive at the same time. Besides if you do that you might as well get a Mac II.
I worked almost exclusively with a Mac Plus and MOTU Composer and Performer back in the day. The GUI is terribly slow, especially when chasing, or if you have complex MIDI tracks, but that is the nature of that Machine. The SE is only slightly faster than the Plus depending on the software. One difference is the hard drive formatting. If you did not format the HD on the SE, you should reformat it as the interleave is different and could slow down access. I also seem to recall that the sound software did not play well with any kind of RAM cache, disk cache, or RAM doubler software, so try disabling any of those things which may be active and see if that improves performance.
When the SE & Mac II came out, the SE was NEVER a consideration as a replacement for the Plus, we went straight to the Mac II, as it was the only real improvement for music use, despite the considerable cost. The SE/30 became an extremely popular Mac for music as it was compact enough to go on the road and powerful enough to drive the most complex MIDI sequences.
Hard as it is to believe the Mac Plus was state of the art for music production until 1987, and musicians were forced to work within the limitations of the technology. Frustrating as it was, it was miraculous, and though we complained about it, we considered ourselves lucky to have access to it. By comparison the Mac II was a god-send, even though by today's standards it's like programming music via that little LCD window on a DX7.
One last thought, is the GUI slow overall? I mean is it slow when just working within the Finder, no other software loaded? Until 6.0.8, it should be quite snappy. If so, that definitely points to a HD interleave problem, a mouse problem (in which case it needs to be cleaned), or worse case scenario, a problem with the ADB interface on the logic board. I'm not aware of any other common problems that would cause an overall lag in the GUI.