Just purchased a 98 4.6 Convertible

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Yes. Look for the casting numbers on the cylinder head castings. Should be PI.
Having to install a new timing cover and its starting look like I have a frankenstang. I'm pulling parts from whats suppose to be an 03 engine but idler pulley is from 97,alternator was off a 98 (not top brace) the coil packs are out front with 4 on each side instead of individual coil packs per plug so pre 99. Lol. Its nuts. Thanks for the help wmburns.
 
but idler pulley is from 97,alternator was off a 98 (not top brace) the coil packs are out front with 4 on each side instead of individual coil packs per plug so pre 99.
IMO you may have some misunderstanding of what you should be seeing. The long block may indeed be from an 2003, BUT the PCM and electronics are still from a 1998. Therefore the motor needs to look (electrically) like the original. Which means a coil pack ignition system.

If you are expecting COP ignition because the motor is from a model year with COP ignition this would be incorrect. The PCM would still be expecting to control a coil pack ignition as well as the wiring harness would have wiring to support a coil pack ignition.

What's the difference? For one a COP PCM would have (8) coil drivers where as a coil pack PCM will have only (4) because of the waste spark system.

Because the resulting motor "package" needs to look like the original, I would expect it to have the same alternator for the same reasons.

This all sounds correct to me. So unless you want to pull the intake manifold to look at the shape of the intake ports, it would seem to me that looking at head casting numbers would be much easier.
 
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