Q-factor and knees.
 

Should my knees be directly over my pedals when I'm riding?
Presently they are out to the sides a bit.

I've been having knee since I bought my new bike.
The old bike was a 53cm with 165 cranks.
The "new" bike is a 52cm with 167.5 cranks

I've replaced my old pedals with a pair that have more float too.

I'm wondering if my BB spindle is too short, which seems kinda wierd.

any ideas?

Are you naturally a little bit splay footed? If so, having to turn your feet inward for a low-Q setup will cause bad patellar tracking and knee pain. Crank length differences this small is probably not a huge factor unless you have short legs. Float can actually cause more pain because you can move your feet (and therefore knees) all kinds of bad ways, most people whose knee pain is cured by high float pedals would have done better to just dial in their cleats a little more, but if it works run it.

YMMV

I'm 5'8, and most of that is my torso. Perhaps it is the crank length, but my geared mountain mike has 175mms, which never give me problems.
I thought more float would help, but I'll try it set up with less float.

I mean, the float is great if you float yourself into the position that your feet need to be in for your knees to be happy and stay there, but movement during the stroke can be really awful. One thing that really helped me get this sussed out was taking a test ride with my shoes strapped down too tight so that my sole definitely moved if my foot moved at all, it sounds dumb but it really helped me figure out WTF was going on down there.

Wow, I would love to h ear more about your knowledge on pedal cadence, leg angle and knee health. It's something I can't seem to bother to look up nor read up on. However, you seem to know alot more than I do.

Q-factor may not be quite as important as the angle of your footbed. If your pedal/shoe combo is angling your leg outwards from the center of the bike, your knees will make a figure 8 shape through the pedal stroke and cause pain and irritation in your tendons. If this is the case, think about getting some specialized BG insoles.

There are potenialy quite a few other issues when changing to a new bike, saddle height and fore/aft position will also affect your knees.

When setting up my new track bike, I tried to emulate the position of my old one, but even the give in the saddle of the old one meant that when copying dimensions, I put the saddle about 1cm too high on the new one, and this alone caused knee pain. Dropping the saddle down that 1cm has resolved it now.