Mac Mini mid 2011 (5,1) 2.3 GHz i5, 2 GB ram running 10.12.1 with 149/500 GB free.
In application monitor everything (memory, disk, network, cpu usage) is nominal.
Disk check (Cmd+R at boot) - Passed
Hardware test (opt+D at boot) - Passed.
On boot the screen goes white after 45 seconds (half of the boot loading bar) and the dock shows up after about 5 minutes. The top bar take lot longer.
Safe mode - still slow as molasses. 78 seconds to launch a new Finder window. Over 5 minutes for System Preferences. Over 5 more to launch any of said preferences (if they don't fail to open)
Already reset the SMC and PRAM. Turned off all spotlight indexing though that wouldn't affect safe mode. Nothing plugged in besides a keyboard, mouse, monitor and Ethernet cable. Tried single sticking each RAM module. Really banging my head against the wall here. Even ssh'ing in from another machine on the network is a drag. 'ls' of a directory with 12 files takes 4 seconds.
Oh and Console keeps crashing. Because of course.
Could anyone recommend a next step?
EDIT: output of vm_stat after a fresh boot into safe mode
Mach Virtual Memory Statistics: (page size of 4096 bytes) Pages free: 3827. Pages active: 103786. Pages inactive: 100841. Pages speculative: 3730. Pages throttled: 0. Pages wired down: 118363. Pages purgeable: 0. "Translation faults": 4213483. Pages copy-on-write: 1353750. Pages zero filled: 779909. Pages reactivated: 566180. Pages purged: 9028. File-backed pages: 69729. Anonymous pages: 138628. Pages stored in compressor: 526296. Pages occupied by compressor: 193246. Decompressions: 310835. Compressions: 1264824. Pageins: 837784. Pageouts: 1602. Swapins: 2409. Swapouts: 3813.