You can't get a Warmoth body and neck for less then a used MIM standard. You can barely get the neck at that price.

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Your pain is the breaking of the shell that encloses your understanding. It is the bitter potion by which the physician within you heals your sick self. Therefore, trust the physician and drink his remedy in silence and tranquility.-Khalil Gibran

Hello, Let me try to help as i own the top of the line MIM,
still the neck is not perfect, and to get it right, it needs a lot of fret work.
a new neck, say form Wormouth will cost you $300 easy.
What i did was find a 84 MIJ neck and add it to my 07 MIM body,
one of the best necks Fender every made IMO. the stock pups are vintage noiseless,
very nice for what i like, i never resell my guitars, so resell prices are not a worry for me,
but i always save the original parts, as you never know what the future my bring.
Mods are nice, but just save the original parts as you can always restore it back to stock if your ever going to resell it.

On here you will 2 types of opinions, 1 from players and another from collectors.
collectors have valid opinions as they buy a guitar for art, something pretty to hang on a wall,
or to brag that this was owned by so and so player. A real player does not give a rat's a $ $ what it looks like, just how it plays,
and in time everyone learns what they like, and will only buy a guitar by how it feels to them.
so if you feel the need to save a buck, buy the MIM and do what you like to it, you can't go wrong.

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1986 Kramer Baretta
1989 Samick "The Samick" Les Paul
2007 Fender Strat MIM Deluxe / 1985 MIJ neck
1990 Epiphone Strat
Marshall JCM 2000 DLS 50 watt / Marshall 1960a 4x12

https://soundcloud.com/jim-slimjim-cassi

I bought a very nice Warmoth neck for $235 and an ash body elsewhere for $99.

^^^^^This

I recently got a 87 MIJ strat by Squier (Fuji Gen). I love this guitar. The electronics have been changed out and she's got some nice Alnico V's in it and new pots, but good grief, the neck on the thing is out of this world. I buy guitars to play. In my opinion, find a guitar that feels good to you. Then mod it to get the whole package. I would gut an American too though so pups mean nothing to me anyways. I don't buy in hopes of making money on it later.

I'd just buy an American Standard or a Deluxe Players Stratocaster (MIM).

I think both of the above would not require any modifications at all (except for strap locks). Maybe you can find one of these used?

Good luck!

No need to get snippy, bro. You started a thread asking about pickups you might get for a guitar that you don't have. So excuse me for being more helpful in your hypothetical situation. But, I can tell you that this is what you do:
First, get a guitar that you like.
Next, use the internet machine to get the specs H/M/L and voicing for the pups you have in the guitar. You can also find sound clips of different pups online.
Use that info as a base to determine where you want to go with your sound. i.e., if you want more mids, look for a pup that has more mids than the ones you have. Maybe you want alnico 2 magnets instead of 5.
After that, post a thread on a guitar forum with some actual information about what you have and where you want to go.
All those guitars that you mentioned, MIM, MIA, Hwy 1, and Am Spec all have different pickups, so how am I supposed to tell you if the Custom 69s are better than one of 4 guitars that you might get? In closing, the CS 69s are custom pups made by an awesome company. They are going to be better quality than many of the stock ceramic pups you will find in cheaper models. However they are not necessarily going to be your key to tone heaven unless you have the right guitar to put them in, which you don't.

CP '60s has what you want...

for me just try them in a store. just like me. i when at my guitar store to buy americain and i try 3 different model (american standard with rosewood fretboard and one with maple fretboard, the other was americain special with rosewood fretboard and one with the maple fretboard and to finish the MIM with rosewood fretboard and one with the maple fretboard) and i don't know why but both americain was horrible in the sound and the neck was horrible and the special was the worse for the neck. i probably get some monday or friday model. but the MIM with the maple fretboard was fantatic, the sound was woow and the neck feeling was great. i bought this guitar instead of the americain. and of course i try all on fender hot rod 1x12. for me you need to try is not just because is stamped usa in the back is mean is better than the other model. first you need to try all the model they got in the store to find the one fit you better and don't get fooled by the seller to try to sell you the most expensive strat. and don't be shy when you try

I installed a set of Fat '50s, and replaced the pick guard, p/u covers, knobs, 2 pots and capacitor in a new Rosewood fretboard Deluxe Player. It does sounds great!

Are you talking about the MIM Deluxe Player? If you are then that is far from the top of the line MIM. The Jimmie Vaughan, KWS, Robert Cray, Buddy Guy strats, the Classic Players and Road Worn are the top of the line MIM guitars. The Deluxe Player is a step up from the MIM Standard.

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Your pain is the breaking of the shell that encloses your understanding. It is the bitter potion by which the physician within you heals your sick self. Therefore, trust the physician and drink his remedy in silence and tranquility.-Khalil Gibran

I wasn't talking about Artist series MIM's, just your stock versions that are available.
and the Deluxe Player is the best of the bunch.

_________________
1986 Kramer Baretta
1989 Samick "The Samick" Les Paul
2007 Fender Strat MIM Deluxe / 1985 MIJ neck
1990 Epiphone Strat
Marshall JCM 2000 DLS 50 watt / Marshall 1960a 4x12

https://soundcloud.com/jim-slimjim-cassi

Yeah no. There are much better MIM that are not artist line like the CP 50's and 60's, Classic series, road worn...

_________________
Your pain is the breaking of the shell that encloses your understanding. It is the bitter potion by which the physician within you heals your sick self. Therefore, trust the physician and drink his remedy in silence and tranquility.-Khalil Gibran