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Can I change the displacement?
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Yes there is a 3.6L version of the 104 engine, but they get rarer by the day.
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Can I fit high flow parts for intake & exhaust?
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Intake wise its hard to beat the OE engineering. You may be able to free up the exhaust a little with a custom system, but I'd be surprised if you could tell from the driver's seat.
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Any turbo or super charger options?
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Yes, custom or custom. 
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Does the computer severely limit what’s possible?
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Pretty much. Although standalone options abound 
I think the best advice is to pick a direction and go for it. 6-8 PSI of boost will get you over 300HP pretty easy and not be a ticking timebomb. Transmission wise a competent basic rebuild should be adequate for the power you're targeting.
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90 300TE 4-M
Turbo 103, T3/T04E 50 trim
T04B cover .60 AR
Stage 3 turbine .63 AR
A2W I/C, 40 LB/HR
MS2E, 60-2 Direct Coil Control
3" Exh, AEM W/B O2
Underdrive Alt. and P/S Pulleys,
Vented Rear Discs, .034 Booster.
3.07 diffs 1st Gear Start
90 300CE 104.980
Milled & ported head, 10.3:1 compression
197° intake cam w/20° advancer
Tuned CIS ECU
4° ignition advance
PCS TCM2000, built 722.6
600W networked suction fan
Sportline sway bars
V8 rear subframe, Quaife ATB 3.06 diff
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