While this is definitely a cheaper way to address the problem, what you're essentially doing is disabling a system that Mitsubishi's engineers spent a lot of time and effort to develop in the process of making this engine one of the most powerful engines for its size that was available in the mid-90's. Auto manufacturers don't typically add complicated systems to vehicles unless they make a significant contribution to the vehicle - a factory rep for Nissan once told me "Parts that we can leave off of a vehicle don't cost anything to manufacture or install, and they never come back for warranty repairs" If Mitsubishi didn't think the system's benefit outweighed it's cost, it wouldn't be on the engine in the first place.

Some people have removed the variable intake system butterflys and plugged the holes and have said that they don't notice a difference in performance afterwards. I will guarantee that before and after dyno runs would confirm a loss of torque at lower rpms due to the loss of the longer tuned intake runners. There's a reason that virtually every modern 4 cylinder engine on the market today has the same variable intake system technology - the longer, tuned runners increase the engine's low end torque.

I think that it might be worthwhile to check with some local machine shops to see if someone could fabricate some replacement bushings for your lower manifold - I don't think it would be too difficult to disassemble the butterfly and shaft assembly and install some brass bushings, and it could easily be a lot cheaper than a replacement lower manifold - you would just have to deal with the additional downtime. I've kept my old lower manifold after I replaced it for exactly that reason, I just haven't had the time or the need to pursue it.