[dtw]

Let's hear more about the backfiring and sputtering...under what conditions (rpm, load) is it occurring? How does the engine run otherwise? Other issues that will come into play with your symptoms:
-What are the results of compression and leakdown?
-Did you properly time the injection pump?
-Have you gone through check/measure/adjust?
-Are you getting good fuel pressure out of the injection pump to all injectors? What is the condition of the pump? How long was it out of commission? Was it stored properly?
-Is the ignition timing good?
-Are the plug wires on in the right order?
-Are the throttle bodies on the right side in good repair? Worn out throttles will cause problems at idle like you are experiencing.
-Are you backfiring through the exhaust as well or just the intake? Have you checked your plugs, and are you getting combustion on all right bank cylinders? A dead hole could result in unburnt fuel lighting off in the exhaust.

Just had the problems you indicated after building a 'boxed' engine just like you had! So I can relate, and can assure you that I had to address all the above questions between myself and my mechanic before getting the engine running right. Turns out that:
-the injection pump was no good, and resulted in one completely dead hole
-most of my plugs were fouled
-my injection pump timing was way the hell off, resulting in very rough running on the remaining holes
-mixture was way off
-plug wires on 2 cylinders were crossed up