Dodge V6 3.9 won't run

Just rebuilt Dodge V6 3.9 engine. Engine was running prior to rebuild with 300K miles on it. I am reasonably knowledgeable shade tree mechanic with about 10 rebuilds under my belt. No fuel injection experience. Engine sputters and stops, never starts. ODB II reader indicates no problems “PASS”. However ECM is setting code “11” and reads out by blinking check engine light, but ODB II reader does not see this. ODB II reader will reset this error even though it does not see it. Code 11 indicates either erroneous crank signals , too many misfires, or outside adjustable limits. This is what I have done. Verified flex plate installed correctly ( only 1 way to get it attached). I would bet my right arm that the cam shaft to crank shaft timing is set correctly, no way to see it now. Engine was flooding badly, this stopped after replacement of temp sensor. No spark until I replaced the crank sensor. Also replaced cam sensor, no change. Indexed distributor using voltmeter and standard procedure. Verified indexing of distributor firing order visually by comparing to identical working engine. New cap and rotor, that worked prior to rebuild. Verified fuel squirting out of each injector. Verified throttle position sensor. Truck sat with ½ tank of gas for 9 months during rebuild (I am not usually that slow but stuff happens) Could it be stale gas? Fuel pressure measures good, 46 PSI or so. Hate to spend much more $$ on it, but my ego stands in the way of giving up. I humbly ask the community for help, I could not deal with having the neighbors see it towed off and donated. Too many of them have been annoyed too long by air tools and cursing.

I have another question. Can I put the computer from my working Dodge Dakota STD trans into this Dodge 1500 to test the computer. (would the engine at least run?) They both have V6 3.9L engines which are virtually identical. The Dakota is a std and the 1500 has an automatic xmission. There are different model numbers on the CPU's but the connections seem to be the same. Thanks

if the crank/ flex plate route doesn't work, try checking the compression. the 91 in my sid just got back to gether had the same prob. turns out i flubbed up the valve adjustment. mike