Important points:

1. Red John knows about the phone bugs. Jane has no doubt about this and
says so, so why should we as viewers have any doubt that RJ knows about
the phone bugs. If he sets a trap for Lisbon as part of his killing of
Partridge, he would obviously leave his bugged phone at a different
location. The location of the bugged phones on Lisbon's computer screen is
therefore not a clue worth paying attention to.

2. Bertrum's weirdness at the beginning of this episode can be ignored. Heller is not so stupid to feed us obvious clues like this. As usual, this is just classic narrative spicing. Each episode he will likely make a different suspect a little more suspicious. Ignore.

3. Partridge may not be dead, but he is not the person who attacked Lisbon. The door to the bathroom opened while Partridge was on the ground bound with packing fasteners. Whomever attacked Lisbon was either RJ himself or an accomplice - but clearly not Partridge. I would very highly consider Partridge dead, and I see no reason for Heller to be so deceitful about this. In the post-mortem interview with Heller, he clearly states that RJ needed BP dead at this stage of affairs to complete his grand plans. We should try to understand why this is, rather than consider that BP faked death in an elaborate 2 man operation.

4. RJ holds the bloody blade used to cut BP in his left hand as he wipes blood from it with his right hand, and then smears the smiley face on Lisbon with his right hand (or so it appears). This may be a clue.

5. The room with the 7 pidgeons in it, and with 1 flying out -- this is a clever cinematic device, but if this is indeed the "clue" that Heller refers to, it is weak sauce to say the least. In fact it does nothing but tell us what we already know and are just finding out -- that there are 7 suspects, and now less 1. Are we meant to conclude that RJ is planning a really cool murder scene - so he lures BP to a condemned house and to kill him, and also goes to the effort to plant 7 birds in a room to be a cool metaphor for the 7 suspects in the assumption that Lisbon (or later Jane) opens that room and counts the birds and thinks how clever RJ is?? ... to me, this is just clever (or perhaps wanky) directing by Heller as a 'wink' at the audience. It surely holds no significance.

6. Not really a major point to think about, but it's lucky that right as L is about to open the bathroom door, BP makes a groan in the closet so that she goes there instead. Had she opened the door she would have seen RJ and would have been killed by him (no way he can let her live then), and then the whole Partridge element of the plan would have been wasted. Lucky that BP groans? I guess so.

7. BP saying "tyger tyger". Was he told to say that? Not possible. Most likely this poem was recited to him by RJ as he was killing, binding, and forcing him in the closet. So it is the only clue BP can think of to tell Lisbon as his dying utterance. We must assume BP never sees RJ, as RJ would never let this happen or he could just i.d. him to Lisbon as he dies. RJ must have planned for BP to be able to say a few final words to L and wanted to plant the "tyger" clue deliberately.