another noob trying to tune the servo

Are you sure you have disabled all power management in the BIOS?
Disable Cstates >1
also disable legacy USB
2 MS delays really suggest power management issues
It may also be a bad hard drive (do you see error messages in the kernel log?)

latency run result:
RTAI Testsuite - USER latency (all data in nanoseconds)
2018/09/19 17:43:21
RTH| lat min| ovl min| lat avg| lat max| ovl max| overruns
RTD| -1456| -1456| -1435| 3192| 3192| 0
RTD| -1456| -1456| -1234| 1968684| 1968684| 19
RTD| -1456| -1456| -1434| -1039| 1968684| 19
RTD| -1456| -1456| -1434| -735| 1968684| 19
RTD| -1456| -1456| -1237| 1963638| 1968684| 38
RTD| -1456| -1456| -1434| 3530| 1968684| 38
RTD| -1456| -1456| -1234| 1958281| 1968684| 57
RTD| -1456| -1456| -1436| -780| 1968684| 57
RTD| -1456| -1456| -1236| 1959735| 1968684| 76
RTD| -1456| -1456| -1437| -1045| 1968684| 76
RTD| -1456| -1456| -1435| -777| 1968684| 76
RTD| -1456| -1456| -1236| 1956089| 1968684| 95
RTD| -1455| -1456| -1433| 2611| 1968684| 95
RTD| -1456| -1456| -1238| 1952266| 1968684| 114
RTD| -1456| -1456| -1436| -735| 1968684| 114
RTD| -1456| -1456| -1236| 1946340| 1968684| 133
RTD| -1456| -1456| -1435| -1076| 1968684| 133
RTD| -1456| -1456| -1434| -751| 1968684| 133
RTD| -1456| -1456| -1236| 1947316| 1968684| 152
RTD| -1456| -1456| -1437| -1056| 1968684| 152
RTD| -1456| -1456| -1238| 1938992| 1968684| 171
2018/09/19 17:43:41
RTH| lat min| ovl min| lat avg| lat max| ovl max| overruns
RTD| -1456| -1456| -1433| -793| 1968684| 171
RTD| -1455| -1456| -1237| 1934986| 1968684| 190
RTD| -1462| -1462| -1438| 2602| 1968684| 190
^CRTD| -1462| -1462| -1438| 2602| 1968684| 190

Also tried disabling lan, usb, ide busmaster, everything non essential, same latencys
Killing Xserver, same
Init 1, also same results

Is there a better way to pinpoint where the latency may come from?

the Latency FAQ post says that the SMI latency spikes are regularly between 32-64 secconds, but I have them in 1-3 seccond period

Disabled CStates, legacy and also tried booting from a pen drive, no difference
Hard drive is a 32gb SSD

Can you download and boot Linux Mint Mate version, in the preferences menu there is an entry named "disks", open that and do a benchmark of the said SSD, check that the read and write lines are linear with no spikes, if there are huge spikes it points to serial ata problems on the mainboard. Had a fair share of those.

It was the SMI!, after unsuccessfully tried to recompile the smi module to accept the ich10 chipset, just downloaded the smictrl tool and this was the result
## RTAI latency calibration tool ##
# period = 100000 (ns)
# average time = 1 (s)
# use the FPU
# start the timer
# timer_mode is oneshot

RTAI Testsuite - USER latency (all data in nanoseconds)
2018/09/19 19:23:48
RTH| lat min| ovl min| lat avg| lat max| ovl max| overruns
RTD| -1457| -1457| -1436| -878| -878| 0
RTD| -1456| -1457| -1431| -667| -667| 0
RTD| -1456| -1457| -1430| 2759| 2759| 0
RTD| -1455| -1457| -1435| -916| 2759| 0
RTD| -1456| -1457| -1438| -997| 2759| 0
RTD| -1456| -1457| -1431| 3546| 3546| 0
RTD| -1456| -1457| -1435| -687| 3546| 0
RTD| -1456| -1457| -1436| 2710| 3546| 0
RTD| -1456| -1457| -1433| -1021| 3546| 0
RTD| -1456| -1457| -1430| -645| 3546| 0
RTD| -1458| -1458| -1437| -682| 3546| 0
RTD| -1456| -1458| -1437| -782| 3546| 0
RTD| -1456| -1458| -1437| -897| 3546| 0
RTD| -1456| -1458| -1429| -642| 3546| 0
RTD| -1456| -1458| -1435| -902| 3546| 0
RTD| -1456| -1458| -1433| -1005| 3546| 0
RTD| -1456| -1458| -1434| -680| 3546| 0
RTD| -1456| -1458| -1432| -662| 3546| 0
RTD| -1456| -1458| -1437| 3554| 3554| 0
^CRTD| -1456| -1458| -1437| 3554| 3554| 0


also added this simple script to init.d:

#!/bin/sh
### BEGIN INIT INFO
# Provides: blabla
# Required-Start: $syslog
# Required-Stop: $syslog
# Default-Start: 2 3 4 5
# Default-Stop: 0 1 6
# Short-Description: blabla
# Description:
#
### END INIT INFO

smictrl -s 0