If your final finish is going to be gloss, you could probably get away with overcoating your canopy. However if the final finish is to be flat or semi-gloss, don't even think about it - you'll screw up the canopy. I usually leave the canopy off until last and mask off the cockpit instead.
Anyway, you have the basic idea in mind,
1. Apply a coat of clear gloss and let dry (24 hrs minimum - 48 is better)
2. Apply your decals and let dry for 24 to 48 hrs
3. Apply clear overcoat of choice (Gloss, Semi-Gloss, or Flat)
4. Remove any masking and install any remaining items (Canopy, antennas etc)
Question: Rather than use Tamiya Clear, why don't you use Future as your Gloss base coat? (I'm assuming you are using an air brush). Simply spray it on like you would any other coating.