Don't know if you've looked into this yet but at the bottom of the timing belt housing lies the crank position sensor.  Is there any oil leak there?  Bad front seal (caused by wear or by bad keyway and timing cog wobble) will cause oil leak on crank position sensor and result in engine miss.  Happened to me.  Miss was always bad until engine warmed up and oil was slung off the timing cog.

It looks like Mr Fuelish was on the right track(er)!  Talked to the service manager at a local garage I took it to. 

They ran most of the same checks I did, and came up with nothing (make sme feel good, but might ahve been cheaper if they had found something).  Then they ran smoke into the intake manifold and watched for -- well, smoke!  Had it coming out of the egr diaphragm.  I don't know if I didn't catch it due to not testing it hot enough or what, but that's todays prognosis.  Will see tomorrow afternoon if that was all.  If that's it:  $355 smackeroos.  Could have bought a Lockrite for that!  Or a pair of new struts (more likely). 

Ok, replaced the eGR.  $179 for it!  Plus the gaskets and time to do it.  And an additional $63 to read the codes.  I understand paying time for troubleshooting, but not for a 5-15 minute job.  Especially when all it told you was 'multiple engine misfires'.  They told me it was mostly fixed with a mild miss and may need a new distro (that's the way the pickup and coil assy are sold) for $300 and labor.  So I wento NAPA and bought one ($200) and spent 5 minutes pulling it, and 5 minutes installing it.  Still it misses!

Thinking I am missing a smoking gun I went around and tightened all intake bolts and checked the egr install (oh, forgot to mention the now broken atmosphperic pressure sensor mount and the drivers door window stuck in the down position -- I told them to not use it).  No joy, so I put a resisitor in line to the engine coolant sensor (ect) to trick it itno thinking it is cold.  It idles a little high (~1200) but at least it doesn't die.  And it still misses under load.

ARRGGH!!!!!

Pulled the timning cover (forgot how much a pita this is) and verified no slip on the belt.

Pulled the intake manifold and inspected all gaskets and air path surfaces. 

Put it all back together and presto!  It still runs like crap when warm.

Couldn't get the factory tune on the idel to work correctly, but probably related to the base problem.

Eieieiei!

I know it sounds stupid but my buddy had the same problem with a sunfire he tried everything
started replacing stuff left right center
I said bring it over lets have a look
start at easy
check plugs wires coils he said no those are only two months old
Ok I will do timing it was spot on two hours later checking everything I said this is stupid
I am checking the plugs and wires grounded the plugs one at a time and checked the spark
2 out of 4 were firing erratic used a couple of donner wire and checked again and presto spark
the thing just ripes
it sounds like timing or spark does it miss fire under a load or just at idle?
if its load then its wire if its idle then timing or combo

just a thought start simple

Dustin

Well, thanks to a fellow member local here (I emptied my messages too completely, so I can't give him credit -- thanks a bunch for Parker Imports; Stan was great and fast). 

I now have a $175 set of $40 spark plug wires.  But that's what you pay people for.  And probably $500-$600 in repair and parts, and a lot of my hours in finding  this problem.  Now I have a shop for those times I am lost. Yeah!

To recap, I had the thermostat stick closed in early/mid December.  Replaced the thermostat that day, but the vehicle started running poorly when it was warm (only), then got worse as time went on.  I spent a lot of time troubleshooting and finally took the vehicle to a local shop.  They ensured me that they had fixed most of the miss and wanted to replace the distributor for $300 plus labor.  I decided that if it was indeed running so well a little miss was ok for a few weeks until funds came back up to level.  I picked up the vehicle on the way to work (don't do this -- no time to review any issues;such as a window that was now stuck down, despite written orders to not roll window down for this very reason).  Found that when it got warm it was running as normal, and all they had really done (besides the egr) was crank up the idle (and left the cap off; next to find one of these).  And broke the atmospheric pressure sensor off its mount.  clearly they had not driven the vehicle adequately before and after the repair.

After getting home and inspecting under the hood (finding the above) I called NAPA (a reason I went to the shop was they were a NAPA repair station, so I figured decent quality parts) and found the distro was $200; so I replaced it, no change.  I then removed and replaced the intake, having found no bad gaskets, obvious issues, etc.  Gave up, so I took it to the recomended shop.  Now I have my Barbie Car back!  SOOO much better than my F350 (it has a job:  carry heavy loads, go straight, never pass a gas station).  It does not turn.  It will go to starboard and port, but only under protest.  Barbie is like a puppy:  noisy, jumpy, and spin in circles around that thing.  Very annoying -- works for me.

Oh, almost forgot:  I had replaced wires, rotor (another story here:  two different rotor diameters, must specify), and cap in November with NAPA parts (the wires were mid priced set).  The oem set still worked fine.  The new set  worked fine for a month or so.  Coincidental failure really lead me the wrong way!

Too bad they don't make the good ol' basic two door anymore.

A bad set of wires cost me over $700!

Enjoy!