If the IoM capiatal weapons are as primitive as there warp drives they are in big trouble vs the Empire
The Imperium's capital weaponry would do fine against Star Wars ships. They don't focus as much on energy weapons, but their macrocannons are certainly on par with the turbo lasers we see on ISDs. They also have some pretty powerful energy weapons though on some of their larger ships such as lances (really powerful lasers) and plasma macrocannons. Also, ISDs are shown to be weak against things like missiles and torpedoes, and if there's one thing the Imperium likes to do in space battles, it's spam torpedoes right before ramming enemy ships. And their torpedoes can be pretty nasty, especially melta torpedoes which can pretty much burn through any armor out there.
The problem the Imperium faces though is weapon placement on their ships. ISDs have most of their firepower mounted on turrets, giving them greater tactical flexibility and maneuverability. The Imperium mounts its weapons in fixed positions similar to old Age of Sail ships, forcing them to rely on being able to broadside their enemies which forces their ships to present larger targets to their enemies. It also limits the amount of firepower an Imperial Navy vessel can bring to bear on a target, whereas ISDs don't really seem to have that limitation.
the old EU Star Wars had things like planetary shields which seem t have no equivalents in WH40k.
Planetary shields do exist in 40k, but they are rarely used. Instead, the Imperium focuses its shielding technology on hive cities. Most hive cities do have dome shields that allow them to withstand intense bombardment from both ground-based and orbital artillery. A prominent use of such shielding was seen in the siege of Vervunhive in the Gaunt's Ghosts novels. The shild of Vervunhive was impossible to penetrate and the forces of Chaos had to resort to using a sorcerer to corrupt the governor of the hive and convince him to willingly shut down the shield.
The IoM still seems to use a lot of projectile weapons for example
Yes, but they are very powerful projectile weapons. Bolters are, to put it simply, fully automatic rocket launchers with projectiles that explode after penetrating the target.
And I'll take this opportunity to talk about the Imperial Guard's lasgun for a second. I know a lot of 40k fans rag on the lasgun and call it a glorified flashlight, but it is a pretty powerful weapon on it's own. It's just weak compared to everything else in 40k. Basically, the lasgun has variable power settings, but the higher you set it, the fewer shots you get out of a single power pack. At maximum setting, you only get one shot but that one shot could penetrate 3 meters of concrete and still kill whatever was on the other side of that concrete. Now, I know blasters in Star Wars have variable settings as well, but I don't think they have that wide of a range of settings.
So who wins?
Honestly, I think the two would fight each other to a stalemate. Neither one could successfully invade the territory of the other (remember, the Imperium of Man is more or less unbeatable on defense, but really falters when forced to attack)
Even if the IoM captures SW tech they can't back wards engineer it or produce it anyway either due to it being heresy
That doesn't stop the AdMech from doing it. Even though it is still considered tech heresy, the AdMech still engages in a lot of secret research that not even the Inquisition is aware of. That's how the Imperium got Primaris Marines after all. So if they got their hands on Star Wars tech, I think the AdMech could definitely do something with it.
If you can kill the Emperor of Mankind/blow up Sol you more or less win the war.
Yeah, but that opens up a whole can of worms the GE isn't prepared to deal with. Remember, the Golden Throne is containing a Warp Rift on Holy Terra and if it is destroyed, that Warp Rift will bust wide open into a giant Warp Storm and allow daemons to endlessly spill forth into the material world. So the GE would have defeated the Imperium, only to see its invasion force get sucked into The Warp and become the playthings of daemons. At that point, the average stormtrooper better hope he gets caught by a Bloodletter before a Daemonette gets to him.
Their weapons are big but IDK if they can penetrate ISD shields, or planetary shields.
I think they can, but even of they can't the Imperium can still destroy both ships and planets. How? Psykers. There are sanctioned psykers within the Imperium's military that have been known to destroy entire planets with their minds. So let's say you have the Death Star creeping up on a forgeworld. The GE fleet supporting it blasts through the Imperium's defenses and now the Death Star is preparing to turn it into the next Alderaan. All of a sudden, the sanctioned psyker on the planet (and just about every planet has at least one) just explodes the heads of everyone on board the Death Star at once.
Of course, in doing so the psyker will probably kill himself in the process or explode in a fireball of warp energy that will then turn into a rift daemons can exploit. But hey, at least the forgeworld wasn't blown up.