Flynn already suspected that Programs could enter the User world long before the ISOs appeared, hence why he put the Portal out over the Sea of Simulation so that no program could accidentally wander through it. Clu wanted Flynn's Disk because it was, essentially, a key to activating the portal. Note that as soon as Sam let go of the Disk, a communication stream shot up from the portal. Before that, there wasn't one.

Think of the portal like a password protected iPhone. When it's idle, it goes to the Lock screen. You can't make a connection to another phone or the internet until you Slide the Bar to unlock it and input the password. That is what the Disk is. It's that little Lock Bar with a password.

As for what a Lightcycle, etc would turn in to in the User world, I think they would turn into what they are but instead of energy and digital cells it would be whatever is possible in the laws of the Universe. Just because we don't have Light Swords and gravity defying dreadnoughts doesn't mean its not possible for it to be translated exactly as that.

Things like the Light Ribbon probably would become magnetic encased plasma that eventually dissipates the longer it gets and the further away from its source.

Can a Lightcycle/Jet form around a controller like it does on the Grid? Sure. Why not? Energy has the same sub atomic properties as solid objects. It's just a matter of solidifying said Energy into a Solid Mass before the controller comes crashing back to the ground in a world of hurt.

I think Clu would have figured out a way to translate his world's technology into the User world exactly as it is before attempting to invade it. Wouldn't do him any good if his soldiers tried to get into Lightjets only to discover that the Batons don't work. Be rather funny actually.