Well first you'd have to stop the mining. Not entirely possible given that mining planets are as heavily guarded as Coruscant. Which even with the chancellor helping the CIS in kidnapping him they were detected and engaed by heavy fleet elements in minutes. The battles lasted long enough for Obi Wan and Skywalker to hyperspace in, formulate a plan and get into and they were hours away from Coruscant at the start of the battle.
Stopping the mining operations is simple. Considering your mining operations are done using droids. These droids can easily be assimilated by the Borg or even have the entire planet destroyed by Species 8472 altogether in a matter of seconds.
Your cloaked ships would be easily detected by SW gravity sensrs not to mention Yuuzahn Vong technology. They would be destroyed long before they could get anywhere near the facilities. Remember only phasers and photns need lock ons to be effective. Turboalsers have human gunners.
How would they "detect" our cloaked fleets if they can't even detect a millenium falcon piggy back riding on the back of a star destroyer? Your sensors are either not sensitive enough or has major weak points.
Are you telling me that human gunners are more accurate then the computer? If this is the case, you wouldn't have the Aegis system in the US Navy. When Luke and Han was trying to fight off those tie fighters using those gun turrets on the millenium falcon, they missed 70% of the time.**Hardly efficient at all.
Star Trek aiming HARDLY EVER miss. Your ships are so large, it will be almost impossible to miss. Your ships are so slow, it will be almost 100% accuracy every single time.
Actually considering the mental make up of these beings they would be infinitely easier to control than even a resisting human. Species 8472 would never get in the fight as SW has no reason to go to fluid space and thus would never be a threat and would even eleiminate two possible threats. the Borg are a collective intellects whos will is superceded and supressed. One Jedi would own the Queen in a mental struggle and thus own the collective.
When Borg drones are assimilated, they become ONE. They no longer have an independent mind for a jedi to control. They'll first need to be severed from the collective. I don't see how a Jedi can use its mind control techniques on the entire Borg collective. Basically this is equivalent to a Jedi trying to mind control a bunch of computers that is connected into one network using a wireless connection. Can Jedis uses its powers to rewrite code? to hack? Not sure.
Of course, the borg has far more advanced technologies then just a simple wireless lan network. lol. Afterall, they did assimilate its technology from thousands of other races.
Why won't the Species 8472 fight the Empire? This is a hypothetically scenario against the Star Wars universe vs the Star Trek universe, so we should debate this as if all species and race were in an alliance to fight off the other universe. If we follow your logic, we can also argue that Jedi or the Federation would never fight against each other as well? The empire will back stab the Rebels when trying to fight off Star Trek forces?
And how would this Jedi get inside the Borg Nexus? Is like a termite trying to get inside an army ant colony trying to assassinate its queen.
And they would be crushed by superior number weapons, technology and firepower.
Technology? Star wars universe is still using human gunners, push buttons, levers, switches and crank wheels. They don't even have touch screens. Most of the droids in the Star Wars universe (r2d2) still rolling on wheels and make beeping sounds. Just like my automatic vacuum cleaner.
Why does it take 200 people to power up the Super laser in the Death star? Why can't the emperor just order Tactical to aim and fire? Who would sit there and let the superlaser power up anyways? Better question, who would actually fight in front of the super laser? This is one of the weakness with the super laser, its too slow and can only target slow stationary objects like planets. Whereas Species 8472's super weapon is mobile enough to be used on anything.
Star Wars tech has stopped evolving when Return of the Jedi came out. Star trek technology has been constantly evolving even after The Original Series. It continues to evolve through The Next Gen, DS9, and then to Voyager which featured Ablative Armor on the Voyager.
With Ablative armor, federation ships could fly straight inside the Empire fleet and shoot at anything at will with quantum torpedoes. Your fleet will have to worry about cross fire and hitting their own ships due to its lack of accuracy by its human gunners. Your huge ships will crash into each other trying to evade our quantum torpedoes or temporal flux torpedoes.