There is likely a black box in there some where, as mentioned trace back to it from your flashing LED.
There is possibly an override switch hidden some place close to the box, used for valet or mechanic to drive without the alarm fob etc.
There is no point keeping the current immobiliser/alarm if you don't have the fob, pull it out and start again with a radio remote central locking box. Mine works fine down under the dash.
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1x CJ8
1x MJ
1x XJ
1x Jeep trailers.
1x Empty Wallet.
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