99 Cobra With Terminator Swap

So I recently bought a 99 cobra that has a 04 terminator swapped engine. The car recently began missing. Replaced the battery because it was bad, alternator checks out okay. I bought a fuel filter, plugs and coil packs, the FRPS seems to be working okay.

My IC pump also was plugged or had air bubbles, and that seems to be working fine now too.

Is there anything else to consider? The fuel pumps are stock 04 with an 04 tank. I don't see any reason that they would not be working okay.

Another question I have... The guy put coil overs on the front, but kept the eibach springs in there s well. His shop told him it was to help support the extra weight of the engine from the swap, but all info I can find states the 99-04 coil overs should work on all applications. SHold I be okay with removing the eibachs and adjusting them?

Thank you.
 
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The 2003/2004 cobra front suspendion had heavier springs to support extra engine wieght due to it being nade of cast iron unlike the any of the other mustangs which have alluminum blocks. This was done because the alluminun blocks wre failing during testing of the super charged engined.