Finally got my PA SOFT 1.4.0 working, please help

[Roman D]

Hi guys, finally got my PA Soft 1.4.0 working. Originally I was trying to install it on my Sony WAIO which is WIN 7 Home, 64 bit. Upgrated to Win 7 Ultimate, installed XP emulator and software just did not work - it would not install drivers. Went to the office, found my ancient Dell 600m with XP, in 5-10 min, I was ready to connect.
I have number of codes displayed, any ideas about fix/solutions/ignore - please reply:
2006, 3.0
DME Module:
E4 (228) O2 sensor controller, bank 2, deviation too great, deviation rich
E3 (227) O2 sensor controller, bank 1, deviation too great, deviation rich
EE (238) Misfire Cylinder 1, Misfiring during warm up, worsening emissions (Misfire carb B_1)EE (238)
EF (239) Misfire Cylinder 2, Misfiring during warm up, worsening emissions (Misfire carb B_1)
5A (91) Exhaust temp before catalyst, bank 1, signal line, short circuit to negative
5B (90) Exhaust temp before catalyst, bank 2, signal line, short circuit to negative
5D (90) Exhaust temp after catalyst, bank 2, signal line, short circuit to negative
3F (063) Control unit self-test 3
3E (062) Solenoid valve, secondary air, short circuit to negative or open circuit.

I had a lean fuel condition with "check engine" light come on and off some time ago and could not pass inspection, Changed original fuel filter, no more "CE", passed inspection no questions asked and later did spark plugs as part of the winter winter prep, air filter is also new. so I went form lean fuel to rich - interesting...

From LCM:
28 (040) Thermal oil-level sensor detect
SHADOW:
58 (088) engine failsafe program
5F (095) check coolant level <<< took may be 100-150 gramm of coolant only so not empty at all