Okay so, I've gotten the kinks ironed out with this Lisa.. the mouse works now, and the floppy drive, although not 100% will format, write and read to disks properly.
This Lisa as mentioned is currently running Macworks. I would prefer to run the Lisa Office System, since to me that's what a Lisa is all about. As far as I can tell, this machine has not had the square pixel mod.
I don't have deserialized (or otherwise) LOS disks. Here is what I do have on hand to help me with the task of putting LOS onto the Profile:
- The Lisa itself and mostly working 400k drive and Profile drive (running MacWorks 3.0)
- A Mac Plus
- A Mac Classic
- A Mac SE
- Mac Color Classic
- LC Network card that works in LC and CC
- Mac LCs
- External 20mb SCSI Mac hard drive
- External Superdrive
- External 800k drive
- Tons of PCs with various hardware arrangements
- Downloaded images of LOS from Raoul's site.
Thinking I had this down, I hooked up the CC to the internet, downloaded the image files, then copied them to my 20mb external. I then hooked up the external to my Mac Plus, ran Disk Copy (which complains that it wants 1600k rather than the 1535k the Plus apparently has, but runs anyway), created the first LOS disk 1 of 5 with it (on a brand new double density disk). Took that disc over to the Lisa, fired it up, but it ejects and won't boot from it.
To test interoperability, I formatted a disk in the Lisa (in Macworks), copied a small text file to it, and then brought it to the Plus. The Plus would not read it -- wanted to initialize. If I erase a disk on the Plus and do the same thing and then bring it to the Lisa, the Lisa cannot read it, and wants to erase, and vice versa. On one occasion, I managed to init a disk on the Lisa, copy a small file to it, and have the Plus read it. But wasn't able to replicate that feat ever again.
So I'm not sure what's not compatible here or what the next step would be. If I had a way to transfer the images directly (ie. via serial), I suppose I could attempt to run Diskcopy under Macworks (?) and then write the images directly on the Lisa. But at present I don't see a way to do that.
I'm just not sure if I'm dealing with flaky hardware or a fundamental incompatibility. I don't know the degree to which Macworks is compatible with the actual MacOS. With no way to test these Lisa boot images except on the Lisa I have, I can't tell if we're actually accomplishing anything or not. And obviously Macworks won't read Lisa formatted disks.
If anyone has any ideas -- tricks I can try, hardware to buy.. I'm all ears. 
Thanks!!
Disks formatted in MacOS should be able to be read by the Lisa running Macworks, and vice versa. I'd stick with using the Plus for this, unless your SE has only the 800k drive, and not the FDHD/Superdrive. Sorry if I'm Captain Obvious here, but make sure when you format the disks on the Plus that you are doing 400k (Single sided)
Lisa will only work with 400K/single-sided drives.* Since it seems you have both the internal and external drive for your Plus, try both drives both for formatting and reading formatted disks from Macworks.
Once you can pass disks back and forth between MacOS and Macworks on Lisa, then you should be fairly sure you don't have hardware problems.
Then you need to be careful about disk formats. I've only known LisaOS disks to be imaged in DART format. DART was the one of the first if not the first image tool from Apple. You can find the DART tool out on the 'net. I don't think DiskImage/DiskCopy images will work, or at best may be images you can feed to DART to make the physical LisaOS disks. If you need DART or known good LisaOS DART images, PM me.
The serialization of LisaOS disks is only for the applications. You can load the basic LisaOS from the 5(?) disks on more than one machine. When you install an application, however, that floppy gets serialized to that one machine (or more specifically to one of the ROMs in the machine). You can use a hex editor to remove the serialization on disks/images if the app images you have are serialized. Google can help you with this.
As far as the square pixel mod, it consists of a small circuit board that was generally sticky-taped to the inside of the cabinet to the right of the CRT neck if you are looking down from the front of the machine with the top off. There's a cable that goes from the board with the CRT adjustment pots to the little circuit board, and then a cable from that to the CRT. You can take it out-of-line by just connecting the cable from the adjustment board to the cable from the CRT, bypassing the small board. Just leave the small board in there in case you ever want to revert to MacWorks.
Hope that helps- if there's any errors here it's because I'm doing it from memory, and it's been a while since I've been inside my Lisas
* - unless you have a special ROM from Sun Remarketing, but then LisaOS will not know how to deal with the 800K drive - it's only for MacWorks. I believe you said you have a LisaLite card in your machine, so that option is out the window anyway - the SunRem mod won't work through the LisaLite card, if I recall correctly.