Just an observation:

The original nuts require a 13mm socket .

The replacement ones from ID parts require a 12mm socket.

This was evident when I had a couple of studs come out of manifold with nuts tight. I had the 13mm socket to replace them then the new nuts would tighten some then give. I then noticed the rounded corners and checked size finding they were 12 mm.

It would probably be a good idea to buy a couple of the exhaust manifold studs if you need to remove exhaust manifold if you want to be able to easily replace with all new nuts the same size.

Similar studs are difficult to source. all the ones I saw at local hardware and amazon etc that are about 36 to 40mm are double ended and have a non threaded area not in the middle requiring a spacer washer or two or three to tighten appropriately. Of course you may be able to use threaded rods cut to length at least until you can source the correct ones it would not be a good idea to count on them indefinitely. ID parts is easiest place and very reasonably priced.. Or you could try to get the old nut off and reuse original. I had one stud come out and one was already broken when I removed manifold because of an escaping exhaust noise that occurred after replacing head bolts with ARP studs maybe tightening head down tight cracked it who knows. Only a couple of very small areas looked like a relatively fresh break on the broken stud surface about size of a toothpick total.

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05 Blu LIM, OME GDE Tbo, wk II 245/75/17, KC Lights, bull bar, 195K H TC
05 Blu Lim, Dayton, GDE HT, 255/75/18 , 210K , H TC
06 Bla Lim, GDE Eco, Destination AT 245/75/17, 151K, H TC
06 D Khaki Lim 126K wkII Eur TC
05 D khaki Lim 145k refurbishing
All CRDS: Fumoto, Lift , Fan Shroud mod, fuel head Gen II, SAMCOS,self TB, 2 Mic filt, Hayden

What length are thread are the exhaust manifold studs. If they are anything like the manifold to turbo studs, which break easily during removal unless soaked in pblaster or some such, you should be able to source new ones and nuts at any parts store. That's where we got new turbo studs.

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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

The studs are right at 40 mm with non threaded section in the center see lil pic they call them 46mm http://www.idparts.com/exhaust-manifold ... -1788.html
All the ones I found in 8mm x 1.0 anywhere near that length had the non threaded section off center so that you needed to use long threaded side in head to make sure it went all the way in and then there were not enough threads to tighten the nut thus the need to add couple of spacer washers

You also cannot use much longer ones in some of the holes due to spacing of turbo etc ID parts lists a OEM part number but seems to say these are a little longer (46 mm)

The only ones I could get locally or easily find other places were made like the exhaust to turbo studs pictured here
http://www.idparts.com/exhaust-manifold ... -3217.html

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05 Blu LIM, OME GDE Tbo, wk II 245/75/17, KC Lights, bull bar, 195K H TC
05 Blu Lim, Dayton, GDE HT, 255/75/18 , 210K , H TC
06 Bla Lim, GDE Eco, Destination AT 245/75/17, 151K, H TC
06 D Khaki Lim 126K wkII Eur TC
05 D khaki Lim 145k refurbishing
All CRDS: Fumoto, Lift , Fan Shroud mod, fuel head Gen II, SAMCOS,self TB, 2 Mic filt, Hayden