Oven cleaner works well, the stuff that comes in an orange box with a plastic bag. It removed 95% of the gunge from my metal-and-plastic 16v manifold, leaving it for 24hrs with occasional agitation. The plastic is unaffected but the alloy takes a bit of a beating in the caustic cleaner, with a sort of brown plating-out of carbon onto the metal. It's a bit ugly, so I sprayed it with silver heatproof paint.
With a blanked EGR and deleted swirl flaps and the EGR mapped out c/o Autolusso, it runs extremely well. There's no shortage of low-down torque at all, it'll pull cleanly and strongly from tickover on the throttle in 1st and 2nd, though that's a bit cruel to the DMF so I don't. However I ran it for a couple of weeks before getting the AL map, and the map made a difference. I am pretty sure they alter the fuel map to suit the greater 02 availability with the EGR blanked. Certainly the engine seemed significantly stronger at low revs, after the map.
If you just remove swirl flaps but keep EGR, yes, I believe you'd lose low down torque and possibly fuel efficiency. Swirl flaps are only there because EGR exists. The idea is to recover some of the combustion efficiency via swirl, that is deliberately degraded by the inhalation of exhaust gas to reduce CO emissions.
The cost of EGR+swirl delete in emissions terms is that at low revs the higher combustion temps increase NOx. But (a)diesels use very little fuel at idle, so a percentage increase in NOx doesn't add up to a lot, and (b)swirls are fully open by 2krpm so the NOx levels are unaffected. There's no impact on soot AFAIK. My car passed the MOT soot test at ~50% of the permitted limit.
Basically, on the 1.9 16v CF4 with metal swirl valves you either delete EGR and swirls before it trashes the engine or afterwards, or accept that you're going to be replacing the cylinder head rather often, or simply scrap the car. I was lucky, I lost 2 flaps but one was stuck in an inlet tract. I had 2 bent valves and a pockmarked head, and my piston damage was superficial, but unlucky that an injector nozzle also got clattered. If I'd had it all repaired professionally instead of DIY, I reckon the bill would have been pushing £2k by the time belts etc are included.
On a 2.4 or 1.9 with plastic flaps there's not the same compellingly costly reason to delete all this stuff, but it makes no sense to remove the swirls and keep the EGR. You just keep all the EGR problems and gunged-up inlet, and make the motor less efficient.