Don't know if the following will help but this is what I did.
My cat was from the Humane Society and they had already microchipped him as a kitten, just before I adopted him.
Being that it is vital to the UK that they are able to verify that the date of microchipping preceded the date of the vaccination that came prior to the blood draw that gets sent to Kansas (whew!), I went back to the Humane Society and got them to issue me with a letter stating the exact date that my cat was chipped by them. I didn't want to take any chances, and wanted to be sure that proof was in writing even though both I and my vet could plainly verify there was already a chip.
I did that because my vet who handled the rest was not the "chipping" vet and yet she had to write into Form 998 the chipping date. I provided her with the letter and she wrote that date in.
Your vet too will have to record the date the animal was microchipped, when he or she conducts the procedure -- you might as well get your vet to write that bit down on form 998 the same day, in the section that requires it (bottom of page 1 if I'm not mistaken).
Also have him or her write into 998 the date of the vaccination if a different day.
Don't have anthing signed or stamped or dated though -- this is the stuff that starts the 4-month validity clock ticking on form 998. You can fill in the procedure dates and details, and the result of the FAVN rabies titre, and the dates of chipping, vaccinating, blood draw -- just don't complete the vet's signature and date of signature, and don't complete the final section on the tick and tapeworm treatment.
One quirky thing -- I was told by my pet transport advisor to ask my vet to please write these dates in the UK format, ie, instead of month/day/year as is customary in the US, the PETS Scheme forms need all dates to be expressed as DAY/month/year as is customary in the UK.
I don't know if that is redundant and perhaps they don't really need that -- all I know is I did it anyway and all went well. I was also told that not just signatures but the whole thing needs to be completed in...blue pen. This is because apparently the UK authorities feel that all black can look too much like a photocopy and they want to know that absolutely everything is the original.
So I went ahead and made sure every thing handwritten was all blue pen all the way, just incase...