Hi guys it went to -5 C or 27 F and I got a CEL on my jeep when I read the codes I got these two codes namely P401 & P299 relating to trans.
Any ideas what caused this and possible fixes, thanks.

Neither of those are transmission codes; in fact a normal non-dealer type scanner cannot pull any transmission codes except the generic P0700 which only tells you that the TCM has stored codes. In fact there is a TSB related to that code TSB 25-001-05 although it calls for what dealers love to do which is replace the EGR when in fact the EGR can be cleaned see viewtopic.php?f=5&t=59352&p=659410#p659410 or viewtopic.php?f=5&t=62495

P0401-EGR SOLENOID CIRCUIT NEGATIVE DEVIATION
P0299-BOOST PRESSURE SENSOR POSITIVE DEVIATION

P0299 can be a clogged air filter, clogged vacuum tower filter (little filter hanging off the passenger side) or a bad boost pressure solenoid (see viewtopic.php?f=5&t=70602&p=757348&hilit=boost+solenoid#p757348) or a collapsed vacuum line see viewtopic.php?f=5&t=61240

However your best bet may be to call or email Keith at GDE and get a GDE tune.

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Sold to LOST member my 05 Ltd, GDE Stg II turbo + TCM tune, SunCoast TC w. Transgo kit, Steiger window regulators, Samcos, Fumoto valve, 2nd gen filter head with Lub. Spec. bleeder, Hayden clutch & 11 blade fan, inverted spare, P-1 battery, BF Goodrich Long Trail TAs, Etecno1 glow plugs, timing belt at 50K miles/8 yrs

Thx for the insight into this I was putting off GDE tune now it has put spotlight back on it.