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Sounds like you may need to change how you drive it...
Short of a catastrophic differential failure (usually caused by abuse/burnouts, etc.), the MTX-IV tranny will usually last quite some time before requiring any more than a clutch. At least one member on here has a '91 with 270K and he just rebuilt his tranny recently (preventatively mind you) for the first time.
You could look into buying a rebuilt MTX from FPS in Georgia or SHO Shop in CA with the Quaife ATB differential, but expect to pay about $2500 plus core. You could also rebuild it yourself, with the parts and video from http://www.shonutperformance.com
What has been the manifestation of the failures you're having?
That would be me. You can see the story and pictures of that clutch and transaxle work here. That transaxle looked beautiful on the inside after 271,000 miles and only the brass blocking rings showed even the slightest wear. It is the original transaxle and has had to bear the burden of pulling a 3,000 pound boat all of its life.
You have either had incredibly bad transaxles (by definition: unbelievable) to start with, or have a driving style that would have to be defined as abusive. Let us in on how you are killing these boxes and what their mode of failure has been.