The Marshall and Les Paul combination is renowed for giving you classic blues/and rock tones.
Using the Stratocaster through a Marshall JCM 900 will sound different, the tones may not be as thick as what you would get whilst using a Les Paul.
Bluestones are not all about being thich and creamy, some people use subtle tones for their chord-and improvising. The Boss BD-2 is a great companion to get some of those tones from the Marshall JCM 900.
Here are some guidelines as how to set up your JCM 900 (or any other Marshall amp for that matter) go for a clean tone, even while you play the strings hard, do not let the amp break up too much. Set up the BD-2 for a trebly tone, 12.15 will do (12.00 being tonecontrol set half way) while you keep the gain control down as much as you can tolerate. Open the gain too much and you will loose the subtle sound from the amp.
When you are doing it right you will get a bit of hair on the sound when you dig in your strings, chords may also give you a bit more dirt, but for the single string notes you should get a clear tone with added brightness. Adding a delay will add a bit of sparkle to the overal sound. Keep your delay out of the range of Slapback, go for glassy tones, but not too much as the sound will get too hollow and echoy.
As for guitars to use to get this sound, single coils may be your best friend. Humbuckers may be too powerful to give you the sweetness, but use this approach as a guideline only.
Happy experimenting and see you soon again,