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Trade for a 98 R/T with 2.4 swap, srt internals, srt turbo, megasquirt, coilovers, enkie rims... ?

It should work fine as long as you get the fuel system taken care of.
A friend of mine turbo'd his focus. His 1st setup was an ebay header. Then he mad an adapter piece for his wastegate and T3 flange. Basically doing what it sounds like you did.

Unless you build up the auto it won't be able to handle as much power as a mtx.