Injury help needed in prep for Ironman France

OK.. at a slightly difficult point here! Have been training for Ironman France (end of June race day) and have been following the Triathlete's Essential Guide program (IM distance level 4).  This weekend called for a 2 1/2 hr run and a 4 1/2 hr ride. Due to travel I ran at approx midnight and was on the bike first thing next morning! I am currently working in Saudi so the runs are now on a treadmill due to the heat winding up (already suffered Haematuria and that was scary enough but resolved!) and the cycling is on a Tacx Fortius turbo (very exciting!!!).  At the end of the cycling this weekend (by the way the weekend in thurs Fri here so bike ride was 3 days ago) I have been suffering pain in my right knee - feels like it is on the left hand inside of the knee cap itself - as is especially prevalent after getting up from sitting and walking downstairs.  Its subsided in last two days but a 10 minute run today started pain again so I stopped.  Luckily I am in a recovery week.  However I am really worried - just about to hit my peak training for my first Ironman (in france so not cheap!) with my brother in law for his first Tri (!) and scared injury could be a pain.  I started RICE tonight.  I suspect Chondromalacia based on what research I have done.  So I have decided to cancel tomorrows turbo sessions for 1:15 hr.  But what advise is out there?  The pain is not real bad - I can push through it right now but is that bad?  Rest - but how long?  hate to screw up all the hard work thus far.... :-(   I probably didn't help the matter cycleing a little bow legged to start due to cahffing from the run!  Bike is new as are shoes but had done some 2:30 sessions with no pain before.  So if anyone can offer advise I would appreciate it.  being in Saudi I do not have access to a decent sports clinic!!!  Feeling so near but yet so far.....