Even though I have a macbook (new) 10 feet from me, I recall the white blinking IR light doesnt flash unless you have it plugged in. You arent voiding the warranty by installing a SSD.
As for the Optibay expansion, I wouldnt but thats just me. Ive done it twice for other people, but if you ever resell it, almost nobody will want that. Also its rather a low key event to pack around a 2TB 2.5" USB HD, now running $120. However that is a subjective choice. I CAN tell you however that the SATA cable used on that expansion is less than ideal and seen more than a few fail miserable. Reliable SATA connectors, oddly enough, are extremely rare on the commercial market in add-on kits, or expasion enclosures.
Since your mac is booting run, running fine, your superdrive noise of the laser-tray reset is normal. I wouldnt worry one bit about the IR light.
*Remember now that you have a SSD,.... to adamantly back it up (always have 2 backups)...... When a SSD dies, it doesnt "fall" like a HD does, with bumps and bruises, ......SSD generally "jump off the cliff" with no recovery possible... i.e. data is genuinely LOST ๐