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All things equal, the 3.5L will always make more power, given that they both have the same identical mods / enhancements, etc.
Members have done a full swap on a 4th gen for less than 6k, another reason why we have this forum, so we could tell the shops and do things on our own, etc.
Can't argue with those facts but... If you want to go FI in an 2000-2003 Max You will have to shell out a hefty premium to do it. Trust me very few people even on this forum do not want to put that much effort and time in themselves to do an engine swap. If you factor in inexperience, lack of facilities, lack of tools and equipment and shear down time do it yourself is not viable option to a lot of people. I know personally whenever I do something the first time it takes me roughly 3 to 5 times the amount of time it takes me every subsequent time I do it. So imagine a job that typically takes an experienced mechanic 15 to 30 Man hours to do; the job could take months to complete. Plus once you are done getting a hooptie to drive around while your car is down and renting all of the equipment necessary even if the work / material bill itself doesn't say 6000 the overall cost to you(Lost time, earning potential etc.) has probably has hit 6000 or pretty close to it.