1st ..... what exactly did he take apart on the old 2.9?
To change the head gaskets you drain the cooling system, remove the upper and lower intake, valve covers, exhaust manifolds and then the head bolts and heads ( *REPLACE THE HEAD BOLTS WITH NEW THE OLD BOLTS HAVE STRETCHED*). Pretty straight forward.
Its a little more in depth but not bad. The distributor comes out and a couple other doodads here and there but you can do it with tools and a Haynes manual in an afternoon or two.
With the new engine.......
Check for proper fuel and spark.
To check spark buy an inline spark tester from an auto parts store and plug it inline with any spark wire you want to. If you see anything but a bright blue spark you have weak spark.
To check relative fuel pressure.....
There is a schrader valve on the fuel rail bolted to the lower intake. Looks like a tire valve stem with cap. Turn the ignition in the on position, remove the cap from the valve, lean away from the valve and use a small flat screwdriver to depress the valve stem. If fuel shoots out in a good spray you have fuel pressure.
If you have both fuel and spark check to make sure your timing is correct.
There are 4 things that you must have for the engine to run at all....
Air supply, fuel supply, spark and timing. If one or the other is a little out of whack it can fubar the whole works. Checking these simple thing will steer you in the right direction as far as which system needs diagnosed.