I have been measuring my deck height in preparation for setting compression ratio once the heads arrive.

Measuring at the center of the piston with no rings

After the first set up I had 1 out of the four that was .012" (#2 compared to #1)less that the others.
I have tried moving a piston and tried various cylinders and got the difference down to .007". the other cylinders don't vary more than .002"

Fearing that a cylinder register has dropped some (case was not decked), when I was changing pistons I laid a straight edge across the registers and I can't see any gaps. I know this isn't the best way to check but my deck height plate doesn't allow me to measure the 2 cylinder heights compared to one another.

So the question is is that too much variation in deck height between 1 &2? Do I need to tear the case apart and have it decked? Is there something else i can measure as another check?

It's in my opinion out of spec. I shoot for combined less than .003" total out of spec. Measure all of your cylinders and be sure they are the same length. That will leave you with:

Cylinder registers
Connecting rod lengths
Crank

Most likely it's either the connecting rods or the registers. I sell a tool that will help measuring the registers, but it's just the plate now and not a full kit.

Crank was checked and balanced so that should be ok.
Rods were balanced and I assumed they were all matched but there is that assumuption thing that can come back and bite you.

I forgot to mention pin height too. Not likely, but worth measuring.

pin height in relation to top of piston?

So I pulled cylinders off and removed pistons so I could lay a straight edge across the registers. I couldn't see any gaps between register and straight edge (checked with feeler gauge)

I also swapped pistons and cylinders around and the Deck height stayed the same on the position in question.

Is there a good way to check for a collapsed register without splitting the case?

So now my question is can the rods be removed without splitting the case?

Thought is if I remove two rods I can see if I can find a difference in measurement and switch places to see if deck height variation follows the rod.

Yes you can.
It is a bit tricky, but can be done.

I went through this exact same exercise a while ago.
However my problem was that I had pistons that measured different deck height front to back

Stu

I am just measuring at the center of the piston.

What was the cause on yours collapsed registers?

Still not sure. I sent it to a machinist and he topped the cases off, but he said they hardly needed any.
The rod guy did very minor striaghtening.

Now the deck is more consistent across the piston, but not perfect:
Here's what I got with no shims under the cylinders:
Cyl#1 Fan side - .025 FW side - .029 Avg 27
Cyl#2 Fan side - .030 FW side - .034 Avg 32
Cyl#3 Fan side - .030 FW side - .026 Avg 28
Cyl#4 Fan side - .031 FW side - .028 Avg 29.5

Stu