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There are a LOT of different ways you could go with regard to alternative engine management.. Only a few that are commonly used though.

You've got a few different options for tuning though. If the investment and labor involved in a stand-alone, ECU replacement (AEM EMS, MegaSquirt, Apex'i Power FC, etc.) is too much you may use one or more piggy-back systems to work with the stock ECU (MAFT Pro, MAP ECU, Apex'i SAFC II or NEO, Greddy.). Piggy-backs often are single or dual purpose devices often requiring more than one device to accomplish significant tuning functionality... Some piggybacks such as the MAFT Pro and MAP ECU provide a level of functionality and control close to that of a stand-alone while remaining less expensive to implement and in some cases much easier to get up and running (just referring to the installation). Tuning any system depends on the person doing the tuning, of course... If you suck at it well, you'll suck whether it's a piggyback or standalone. One nice thing about piggy-backs is that inexperienced people may add one at a time and then take their time learning that particular item and any quirks (there are ALWAYS quirks) without wondering if a certain issue is due to the boost controller, the fuel controller, the after-market timing computer... and so on.

If you do some searching for posts made by me containing "MAFT Pro" or any of a thousand other terms you'll find a couple threads where I go into more detail and explanation about various systems and their hang-ups.