Too late to help now but maybe someone else will benefit. I gel stained my Pella fiberglass entry door 6.5 years ago and it looked great! Used Minwax gel stain and their spar varnish, as directed by Pella. However, it did not stand up to weather at all. It chipped and had to be varnished again every 6 months. This Spring it chipped all the way through to the fiberglass and pulled stain with it! Believe me, I did everything properly. My door faces south east and has no roof. But a neighbor whose fiberglass door faces north had the same trouble - he used the same products as I. My neighbor got disgusted and stripped his down to fiberglass and restained it with Sikkens products 3 years ago. No trouble since. Sikkens makes a Door and Window stain that does not require varnish over top. Fortunately for me, just before I started stripping about 36 layers of varnish off my door, it delaminated! Pella brought me a new unfinished slab (under warranty) and I'm using Sikkens to stain it. I've been told the varnish is the trouble. It's like putting a sheet of glass against the door, trapping the heat. Plus it isn't flexible enough to expand and contract. If I put up a storm door to protect it, the problem would've been worse due to trapped heat. Sikkens is specifically made for fiberglass doors. I don't have any vested interests in the company but thought I'd try to help the next guy... Here is a link that might be useful: Sikkens Door and Window stain

The directions for Therma Tru say that the doors should not be sanded, but I believe this refers to sanding the raw fiberglass skin, not really the finished door. If you sand the raw fiberglass you can either reduce the profile of the grain pattern or you can scratch the fiberglass, both of which may show up when you stain the door. You would need to sand pretty hard to do this though. Lightly sanding and sanding the finish that is already on the door should be fine and this is something you need to do for sure if you are painting over a stained finish.

I like and have used the gel varnish outside, but it was a north-facing sheltered door. The scant UV protection and very low film thickness make it verboten for sun exposure.

I agree with cat_ky, he should order a new door slab and finish it properly. With that may layers of primer and stain it is just going to be muddy looking, no way the grain will look natural. Or get a discount and paint the door...