ok, so the bolts your struggling with, are they nut and bolts..in which case just cut them off and replace...if they are studs/nuts, depending if the studs go through the joint rather than being threaded in exhaust, easier if you can get them undone, but worse case, cut them, drill the studs out and replace with nut/bolts..
dont know the cat set up off the top of my head, but if your talking about the manifold/downpipe studs then pays to spend extra time getting them undone, as if they shear, can be a right pain getting them drilled out and rethreaded or replaced..
I do, (Mk3 Mondeo expert) the cat has captive nuts, (nuts fixed/ welded onto the cat itself) the cat sits vertically and is held on with 4 bolts that go through a plate that is part of the exhaust manifold from the top - there is also a bracket underneath that also has 2 captive nuts+ bolts - the only other fixings are 2 bolts holding the downpipe flange on, the car will need to be raised up (little ramps or axle stands may be enough) to drop the cat/ exhaust down - the threads on the bolts as they come out of the captive nuts underneath are the bits you should be appliing the wd-40
Technically, a decat works better than a gutted cat, as the gasses don't need to expand with a decat + a S/H cat is worth more than a decat, (you could even make a profit) most decats have boltholes that you just use new nuts/ bolts on, that means if you are fitting a deacat you could shear, grind or drill your old bolts off, no problem you don't need to touch the exhaust manifold nuts/ studs to get the decat off a mk3 diesel
A little bird tells me that you can MOT a diesel car no problem (especially a mk3 as it has covers, top and bottom) with a decat even now - Me, i could not possibly comment on that one