I think you hit the nail on the head---timing chain and gears, but the only way to check that is to remove half the engine to get to it. However, if the little dots were aligned, then the timing chain is installed correctly.
Other things to check:
1) Fuel pressure while cranking should be 43.5 psi--too low and the engine might start, but won't run.
2) Are the ignition wires hooked up to the correct Optispark terminal, are they securily attached--double click should be heard.
3) Vaccum lines connected correctly. Most common error is to attach the HVAC line to the manifold where the fuel pressure regulator vaccum line is supposed to go--the engine won't run and if it does, it won't run well.
4) It is possible to connect the injector electrical connection to the wrong injector--engine will run really badly...it's like being out of time.
5) Check the underside of the rubber elbow--has it doubled and into the throttlebody.
6) Read this for checking for vacuum leaks, which can also cause the problem:
VACUUM LEAKS & the LT1
Copyright 2004 by Charles O’Toole
This tech article applies to 1993-1997 Firebird, Corvette and Camaro, including the Impala SS and other automobiles with the LT1 series engine. There is some applicability to the LS1 series of engines and V6s with similar engine management controls.
The LT1 engine is very susceptible to vacuum leaks caused by failures of both vacuum hoses and vacuum control solenoids. The following parts should be checked for a vacuum seal, replaced as needed and definitely replaced after several years of use. The actual age of replacement depends on operating conditions, since hoses and parts fail more quickly with high engine heat and in hot areas of the US (Southwest and Southeast).
1. Check these vacuum hoses and fittings:
a. Two vacuum lines, one going into and one leaving the Vapor Canister Control Solenoid (Right side of the intake manifold).
b. Vacuum line from the EGR Control Solenoid to the EGR and left-hand side of the intake manifold. This line has a common connection at the EGR Control Solenoid.
c. Large, ½” hose leading from the throttle body to the rear of the right side valve cover. Also, replace the plastic elbow—newest design has a small “catch” to retain the elbow in the valve cover grommet. Replace the grommet in the valve cover.
d. If the PCV valve is over 10,000 miles old, replace it with a quality all metal or GM part. Replace the molded, curved ½” hose and the rubber grommet in the intake manifold that the PCV valve fits into.
e. Check that the EGR valve is holding a vacuum.
f. Replace both the EGR and Vapor Canister Control Solenoids. These parts wear out rapidly in dusty conditions and are huge vacuum leaks.
g. Jack up the left rear of the car (Firebird and Camaro), remove the left rear tire and locate the plastic access plate for the Vapor Canister. Remove the small plastic screw with a #2 philips screw driver and the 7 or 8mm bolt and remove the access cover. Check all vacuum fittings and hoses to and from the Vapor Canister. The hoses can dry out and crack, also the nylon vacuum line from the Control Solenoid (right-hand side of the intake manifold) to the Vapor Canister, has a ¼” X 1” rubber hose glued to the end. The glue deteriorates and the rubber connecting hose separates and allows a vacuum leak.
h. The rubber elbow that joins the MAF and throttle Body. These two joints are responsible for most of the vacuum leaks on the LT1. The rubber seal and worm gear clamps can be damaged by incorrect installation. Remove and check the clamp for distortion and nicks, and check the elbow for tears and deterioration. If it is old, replace it and install the new one carefully to ensure a perfect fit. Grease the worm gear to prevent damage when tightening and do not overtighten. (Caution) Do not use silicone grease to ease the elbow onto the throttle body. Check that the small, stainless steel, ¼” tab at the worm gear is not gouging into the rubber seal at the MAF or throttle body—gouging causes a vacuum leak. If it does gouge the seal, bend it up slightly. If the clamp and/or elbow are damaged, they must be replaced. It is impossible to obtain a vacuum tight seal with parts that are damaged.
i. The idle inlet passageway/hot coolant throttle body heater on the underside of the throttle body can cause a vacuum leak. There are several torx screws that come loose, tighten snuggly and use locktite.
j. The black plastic plate on top of the throttle body is a notorious vacuum leak. Replace the plate with one made of aluminum and a thick paper gasket or buy a new, plastic plate. Be careful to not distort the plastic plate when tightening. Use locktite.
k. HVAC fitting at the right-hand side of the intake manifold and the fuel pressure relief valve vacuum hose located on the right-hand side of the intake manifold.
l. Throttle body to intake manifold gasket—torque to 10-ft lbs. and use locktite.
m. The MAP sensor has a rubber seal on the underside. This seal can be lost during replacement or can tear—it is available separately from the MAP.
n. The intake manifold has two vulnerable areas—the intake gaskets and the end rails. The intake manifold bolts should be torqued to 34-ft lbs. in two passes. If re-torquing fails to solve the problem then the gaskets should be replaced. The other problem is oil leakage from the intake manifold end rails. If oil is leaking out, then air is also leaking in, since the PCV valve puts the interior of the engine under a vacuum. All air entering the PCV system must be metered through the MAF. A vacuum leak, even an oil leak, allows air into the system that is not MAF metered air. The same can be said for all oil seals throughout the engine.
o. Power brake canister vacuum hose from the left side of the intake manifold to the power brake booster.
p. The Idle Air Control Solenoid and the Throttle Position Sensor can come loose, use locktite on the Torx screws.
q. It is possible for a loose exhaust header bolt to allow an air leak into the exhaust system. This leak affects the hydrocarbon/O2 balance that is read by the O2 sensors. A leak of this type would cause the engine to run rich rather than lean as the ECM/PCM compensates by modifying injector dwell. Use GM part # 12346004, Teflon pipe sealant (for high heat), or Locktite 272 (hi heat) to lock the exhaust manifold bolts into the head.
r. On 95-97 LT1s check that the distributor is vacuum tight and the vacuum lines to and from the distributor cap have not deteriorated.
s. Replace the o-ring on the oil filler cap and the extension. O-rings are available at Ace Hardware for about 50 cents. Remember all air entering the engine for the PCV system must first go through the MAF, any air leaks, even past an o-ring on the oil filler cap is a vacuum leak!
This is a living document, please let me know if there is something that should be included.
A long read, but maybe it will help.