The Coolant Temperature Overide is designed to open when the engine reaches operating temperature . You don't want an EGR valve to open on a cold engine since the introduction of recirculation will cause an excessive rich mixture that the engine won't be able to handle cold until the combustion chamber is up to proper operating temperature. The vacuum line which is to be connected to the vacuum source should be connected to the carburetor ABOVE the throttle blades so vacuum is not attempting to open the EGR valve at idle . The EGR valve should only open on acceleration . That is when EGR is needed , under load. That is when pre-ignition is experienced due to the absence of lead in fuel . As far as why it was disconnected , I would say it's either dirty and the pointless valve inside the EGR valve isn't closing fully thereby allowing recirculation at idle causing rough idle or stalling along with loss of power or the previous owner or whomever disconnected it believing it isn't needed along with any other engine management systems part of emissions controls that were possibly discarded which is common . Maybe some of the junk that came factory can be discarded but an EGR valve is essential or the pre-ignition ( pinging) will be immediately noticed . Pre ignition is very bad as it is damaging to overheating exhaust valves , pistons ( been know to heavily damage them) , dangerously increase combustion pressure and temperature which leads to engine destruction including cylinder head cracks and blown head gaskets and is just detrimental to performance as well . All mentioned in the way of destruction is extreme and can happen but a responsible owner will notice the symptoms and tend to it before disaster strikes. Please do make an attempt to remove the valve for the purpose of cleaning the port in the exhaust manifold and the pointless valve sealing surface to ensure exhaust gas isn't introduced at idle . Negative back pressure valves can be checked with a vacuum pump to see if the vacuum diaphragm is good but a positive back pressure valve must be tested by blocking the exhaust with something suitable over the tail pipe for a couple of seconds while some one is applying vacuum to the valve and watching the valve open . If either valve dosen't pass either test , replace . If I remember correctly , the negative valves usually were used on a set up like yours as positive back pressures used an EGR solenoid controlled by the ECM or PCM depending on what model year and what emissions control system was used . I believe your jeeps engine should have a negative back pressure valve but just in case it's good to know how to test either. Also , whom ever does the tail pipe blocking should know that holding something like a blanket or towel can only do this for a few seconds as tremendous heat will prompt the test person to quickly let go . It can stall the engine if held long enough but let's not put the test to theory . Safety always .
