My engine went in and out when I was fabricating the engine mounts and positioning the engine. Afterwards I painted the chassis, riveted the floor, routed the brake lines. Then the engine went in again and I did the wiring.
I would sort out at least the attachments for brake and fuel lines prior to mounting the engine/transmission, but other than access in the tunnel and general weight of the whole car you should be fine.
P.S. I pulled my engine twice to sort out an oil leak just weeks prior to my test...
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