Hi,
If I understand you correctly, you have exchanged the mainboards, as the factory calibration is stored on the mainboard, in the flash, in the protected area, a factory calibration is required.
What I mean by this is that the mainboard with all the assemblies connected in RF path is a calibrated chain, if you dissolve it, it is good luck that it has the correct levels afterwards.
How are the levels measured?
Do you have a spectrum analyzer which is still accurate?
Measuring the values with an oscilloscope is one of those things, as the input of the oscilloscope can also have a mismatch.
The measurements are not optimal and you need more accurate measuring devices than an oscilloscope to test these measuring devices.
Regarding the options, I have never had an SML, but it may be a similar procedure to the SMT/SME/SMIQ, i.e. the modulation type is activated with a key.
You can look in the menu to see if they have the item "installation", this is for installing options, these can be entered by deactivating Protect Level 2, at least with the big brothers.
It would be interesting for me to know whether an SML02 can be turned into an SML03 using a factory key.
With the SMIQ02B and SMIQ04B you "only" need a factory key for the 3Ghz or 6Ghz version to turn an 02B into an 03B and an 04B into an 06B.
I have edited your picture to explain the modules, the OPU1 is on the mainboard, the OPU2 is the doppler/trippler module.