I've been aware of how much it costs to work with automatics. If you do it right by getting a performance automatic from the start, you won't have to do any kind major maintence in the future. All you'll have to do is the transmission fluid changes every 50-60,000 miles for around $75. There's no pulling the transmission every so often to work on a clutch or flywheel. Keeping the automatic will save you from those extra expenses plus the costs of swapping to a manual. Also, with the performance transmission you don't have to worry about upgrading it later on because you're putting too much horsepower down to the wheels like you probably would with a manual. How much would it cost for performance parts like clutches and flywheels, cryo-treatment and all the maintence to keep it running well for 60,000 miles?
From my experience, my advice to those of you that have an automatic transmission now is to save your money before you do any modifications to the engine and put it towards the transmission first. You will be very happy with what can be done with just the transmission upgrade. I know that I only have a converter upgrade with a remanufactured Aamco transmission (waste of $2000). With just the stall converter and the bolt-ons, I made my car (94 1.6L) go from 0-60mph in 13 seconds down to about 8 seconds flat. That's a stock SE-R sort of time. The times would be better if I had the performance transmission.
In the performance transmission ($2864) you will have all of their upgrades already in it plus their $400 converter, there's no extra prices to worry about. $3264 is an awesome deal for a customized stall converter (Level 10 will make it for your application, not everyone elses but YOUR application whether it's NA, NOS, Turbo, or Supercharger), throttle oriented shiftkit, valve body upgrade, the super pump, raybestos (blue plate special) upgraded clutches, torington bearings, Kolene Reaction Plates, and possibly the Phantom Grip LSD (not included yet still talking about it w/ level 10, costs $299 from phantom grip).
Anyways, look at the whole picture of things. I think the performance automatic transmission is the way to go if you already have an automatic. I've learned from going through 4 stock automatic transmissions (2 of which I had my Level 10 converter @ 3,200 rpm stall). Do it right from the start or you're little automatic will rape you in the wallet from either gears dissapearing, clutches dying, differentials shattering, overheating, or Factory Nissan converter failures (bearings will die). Get yourself a tranny cooler ASAP to save you from the overheating, it's worth every penny. $20-75 for the cooler will save you from that $2000 rebuild.
Also, if you have a Level 10 converter or any good quality stall converter, don't attempt to go to a local converter shop to raise the stall. When my 2nd to last transmission died because of a broken differential, the junk flowed into the converter. I had to get the converter flushed. So I went to a local converter shop to get it flushed and I was stupid to ask them to raise the stall from the 3,200 to 3,600. They attempted to raise the stall but actually they lowered the stall to 2,500-2,900. My plan is to get it fixed back to the way Level 10 had it and install it again when my engine is replaced by ATK engines for their warranty work (Bad motor).