Hi Sean, all is not lost with the roof. GRP work is something that a competent DIY'er can do very well, there are some rules to keep to thou and a good bit of research into the methods used.
'Pin holing' is what happens when either too little resin is used in the matting stage or even can be from too much toocoat/gelcoat although if too much gel coat it can sometimes lead to crack lines. As the roof has just been laid it is not too late to remedy without removing all your hard work.
Firstly, this description is for a patch repair but is the whole roof is like as you have said for the puddling area then you can just expand the repair area.
Clean the surface ( light detergent only) and dry, you do not want any water contamination within the resin or topcoats.
Sand the topcoat, you do not need to sand through the whole topcoat layer but I do prefer to. This is because if you can see excessive webbing then we are going to remedy that as well as the pin holing.
Clean the dust ( no water) once the dust has gone then thoroughly clean the area with acetone, please be aware of the flash point of acetone and do not roll used rags up into balls etc put away, you must let them air dry to remove the risk of self ignition.
Once cleaned mix your resin as per the ratios based on the Ambient weather temp and the amount you need to use. Use a wool roller to apply the resin over the affected area, allow the resin to dry untill tacky/semi firm.
Once the resin is ready you can mix the topcoat as per above again and roll on with a tighter weave/wool roller.
When you first put the csm down it would have been either 450 GM or 600 GM the higher the GM the more resin you need to apply per sqm.
These figure are quoted on the tins themselves or on the literature supplied.
Once cured you are ready to go.
You mentioned temp, you can use resin from 5c to 30c, it's just the catylist ratio that you change.
If you have any more questions pls feel free to message.
Cheers, Gareth