thanks for your replied, yes I've been watching videos but some are no to used TDC cyl 1 and other says yes, and others using the marks, so its very confusing which to choose without messing up the valves! 
assuming that my r52 was timed correctly the chain marks match in both crankshaft and camshaft with their corresponding sprocket marks, I used a yellow pain to make them more obvious for me, so when I replaced the new timing chain and its components I would have an idea where it was before taken the head off. since then crankshaft has not been moved.

I did used the timing tool to set the timing chain correctly.

here are the pics of the head and the cylinder R52 base convertible

here is the timing marks on the chain and sprocket on my 2006 r52 base convertible,

It sounds like a classic overheated engine...  on an R52 Cooper non-S convertible.

Since you already have the head removed, I would strongly recommend you take the head in for a complete valve job - part of this process will check to see if the head is 'warped' from the heat.  If it is warped, they can machine the head so the mating surface is true.  They can also check for any cracks in the head which may be the cause of the coolant / oil mix.  They can also inspect the valves and seats to see if any work or replacement is required.  

A timing tool may be necessary to set the timing once the head is back on the car.  There may be other methods to set timing, but we have not heard of any other methods to accurately set timing. (marks on the gears and colored chain links have not proven to be accurate).

There are videos on youtube for timing chain replacement.  Look for any video showing R50 R52 R53 Cooper or Cooper S timing chain replacement - they all use the same procedure.

Let us know your progress with this project!

my car was driven couple of months ago by my son and it got overheated loosing power and engine stop. Car got towed to my house, for the last couple of months i’ve Been doing test and the latest was the leak down test. The car was givin p341 error canshaft errors originally and it didn’t want to start up.
im not a mechanic but I have some skills replacing things and disassembling things. So I managed yesterday to remove the crankshaft pulley to make sure that the engine was in timing since it didn’t want to start engine rotates,  fuel and spark was present but the only thing missing was no compression across the pistons.
while doing the leak down test, it  was learned that bubles were going to the coolant reservoirs, and noises over the exhsaust and intake throutle. So I knew I was facing with a blown head gasket and also problems with the head, so yesterday I finally was able to remove the crank pulley with the Chrysler extractor tool, in order for me to find out if still in timing.
On this r52 base cars hardly there is info how to setup the timing, and by researching i found out people has different ways to do it.
so I put some stiff electrical wires over each spark plug hole  to bring each cyl to be even (down stroke) and aligned with the camshaft sprocket one mark and since I removed the timing plate I could verified that the crankshaft also aligned correctly with the timing chain bottom two bronce color matching with the crankshaft sprocket.

i then remove the head and noticed some valves stuck open, one exhaust port and the other set of valve stuck opened on the intake port. I used a flat metal sort of a ruler to check the valve heads and it didn’t noticed a big gap.

thanks to YouTube I have an idea what to look for, my next step is to take the head to be inspected clean and what ever needs repair.

here are my questions
The car has 108k miles, should I replaced all valves? 
Timing chain and sprocket for both crankshaft and camshaft would be replaced, but still wondering about my timing procedures some mechanics said all piston down because this r52 engines don’t time at  tdc cyl 1?
All my piston are set now evenly down no all the way down but enough for my stiff wires to look even at the top!

I noticed in some cyl walls some sort of scratch but when i touch it with my finger, I don’t feel a groove or roughness! or abrasions Should I be concerned?

Or just replaced the head gasket and do the valve job?
Also when engine oil was removed it was milky but I could no find the smoking gun on the gasket no cracks seem on the head gasket.
how do you flush that mess!
Now that I have the engine open and the oil pan it would be replaced I noticed cracks in the oil pan but not leaks.

im afraid to touch or move the pistons because of timing issues, to inspect what are causing in some cylinders  wall those marks.
i would try to post pictures if allowed, I’m using my iphone so screen is not helping me to insert them now.

without creating a big argument  here setting up or check for timing alignment procedures, what are your takes? 

Why there is not information in YouTube when comes for timing alignment on this r52 base engine? 
Sorry for the long post!
I appreciate your time reading it.

gus 
miami Florida