Running without an exhaust manifold or clutch

I'm nearing the completion of a long engine swap project and should have most of the wiring harness finished up this weekend. I'd like to try starting the engine so I know everything was hooked up right, but there are no exhaust manifolds on the engine. The stock ones won't fit, so I have to build custom ones.

The other piece I'm missing is a clutch assembly. I originally put the engine/trans in for a test fit, but decided to build mounts, run lines, wires, etc. while I saved money for a nice clutch and stuff. The engine still has a flexplate on it, so no clutch or pilot bearing.

I only plan to run for 2-5 seconds (no cooling system either). Will I damage anything by starting the engine without these pieces?

If you have a flex plate on there, then you also need a flywheel before you add a clutch.
I would also be weary of running an engine with nothing on the end of the crank.
Usually the flexplate or flywheel is often an important part of keeping things in balance.

I've seen an engine run with open exhaust ports.
I wouldn't recommend it. In your case it simply may not start, or it may start and blow big gouts of flame around.
The exhaust manifold is as critical for removing the waste gas, as the inlet manifold is for getting air and fuel in.

The flexplate is there (LSx 5.3l). I'm mostly worried about damaging the input shaft by not having a pilot bearing, even though without a clutch it won't turn.

I was worried about the fireballs from the exhaust ports. I have alot of wiring near where the manifolds should be. I'd love to hear the engine crack off for a morale boost (this project has taken over a year), but I suppose I should wait until everything is in place. I guess I could just hook up a battery and break out the DVOM to see if things check out.

So, the engine has a flexplate from an automatic transmission on it?

These flexplates are intended to work with the mass of a torque converter to properly dampen crankshaft vibration. This is one reason why a flexplate is so much lighter than a flywheel. So, imo, put a flywheel on before starting it.

As for no exhaust manifold..... that's fine. I have started quite a few engines with no manifolds. It's super-loud, and might melt plastic/rubber in the vicinity if run for a while. But its fine for a few seconds at idle.

I'm not quite as worried about the flexplate issue for a short run... but without manifolds you have two problems - the fireballs (as discussed before) and hot exhaust valves being exposed to ambient air. In those few seconds, the valves, seats, ports, and chambers get pretty hot. Then having direct exposure to ambient air can cause abnormal rates of expansion/contraction.

I don't think a couple seconds would hurt, but I also would be patient and just wait.