If the machine powers on, then personally I wouldn't touch the CPU, just leave it with the socket soldered on top. In the past it may have had some sort of accelerator board, or something like a Vortex ATOnce style of PC emulator board, there were all sorts of upgrades that clipped on top like that.
I'd also suggest binning the top metal shield for two reasons. 1) It isn't really necessary 2) It's a bit stabby and slicey after all that chopping!
The mods are quite possibly factor fixes or later owner applied patches, so I wouldn't be overly worried about them if the machine is functioning as expected.
If you have a 15Khz capable LED/LCD display, then get an UBESwitch from here https://www.exxoshost.co.uk/atari/last/storenew/#0107
and you'll be able to use all resolutions. Also check out Centurion, they also do a similar switch.
If you don't have a 15Khz capable display, then you can still use these switches with any modern VGA display, but only in Hi Res, which is better than nothing.
Regarding the composite sync etc, there is an interesting post here that may be of help: https://www.facebook.com/groups/1331613 ... 024924214/
Be interesting to see what sysinfo makes of that version of TOS.
Also, PSU looks like an SR98, which is pretty easy to recap. I'd recommend you do so.
Collector of old Atari things:
800XL + Ultimate 1MB, 2x 1010 cassette, 1050 + Happy mod, 65XE (128k +APE Warp) & XC12, SIO2SD, 2600jr, 7800 and Lynx II
Atari 520ST (1Meg), 1040STF long button floppy, 2x 1040 STFMs + Gotek, 2x 4160STE with 32Mhz booster, ROM switcher, Mega ST1, Mega ST4, not to mention various bare ST boards for testing including a PAK 68/2
Plus the rest..
Amiga stuff, Mac stuff, Sinclair stuff etc...