Just some FYI observations... a couple weeks ago I took my MG on a 3-day 1100-mile trip, the bulk of which was done in two days of on-and-off heavy rain between which it sat for two nights in some very heavy wind-driven rain.
I'd been in light rain, and sat in occasional showers but didn't know what to expect on the trip, so I took off in this muck prepared for the worst. Packed in the MG were plenty of towels, tape for the header rail, tape for the side windows, and plenty of rain-x on the windscreen. The header-rail seal looked good, the side-pillar seals looked good, I checked the windscreen-to-body seal, it looked good (and there was sealant under it too).
After the first 10 minute downpour on the interstate at 70mph I had two leaks, both coming from what appeared to be the front corner of the door where the bottom of the windscreen meet the vent windows. There was enough water coming in to say it was leaking, but not much more than that. The second was a drip directly over the steering wheel (maybe 6 drops came out). In a horrible downpour the next day the header-rail leak intensified to an annoying level but soon subsided.
On the way home the weather slowly deteriorated. Just north of the Florida border I stopped and carefully stuck a layer of 3M vinyl tape along where the windscreen and top meet, just to be on the safe side (the tape is about an inch wide, sticks like made, but peels off clean and is available in several colors). I'm glad I taped it because I soon found myself in some of the worst rain and thunderstorms I've ever been caught in. I won't bore on with the details (I wish I'd just stopped but I didn't until it was too late), I'll just say the rain was incredible and my minor leaks were proportionally increased in magnitude.
So here's what I found:
* After looking at several MGs at the show I went to I assumed the windscreen pillar seals were trimmed poorly at the bottom allowing water to be sucked into the car at the top of the door. Other than one publication vaguely saying to trim them "flush" there are no real descriptions around about how the seals should be fitted. I've since put new seals on and carefully trimmed them so they match the contour of the door and body perfectly, and when the door shuts it forms a very tight seal. It took about 30 minutes on each side and a lot of trial-and-error to fit them properly, but it's done.
* Unfortunately the leak I suspected in the above case never really, I don't think, existed. The 'door' leak actually was from the windscreen. The windscreen-to-body seal did it's job though (I checked it at a gas-station just for kicks).
The problem was where the pillar meets the bottom frame of the windscreen. Apparently there was enough of a gap somewhere to let water in, and the only place the water can go is just behind the pillar inside the car.
I wasn't about to pull the windscreen out to try and reseal it so I injected flowable silicon into the joint, where it weeped away into the depths of the windscreen/pillar joint. I repeated the process a few times until the weeping stopped and the silicon layered itself along the outside of the pillar. After it dried I used a new #11 X-Acto blade to trim it flush with the pillar, nearly invisible. No more leak.
* The last annoying leak was the dreaded header-rail. I've heard of this one before, which is why I packed the tape. At first glance it seems that the only reason to have a leak is a poorly fitted header-rail seal. I decided to go ahead and install a new one while I was working on it, but when I finally woke up I realized the leak wasn't from the seal at all.
Apparently there was enough water gathering in front of the seal that at high speeds it was pushing over the top of the seal on the roof-side and sneaking over the aluminum strip that holds the seal in place. Mine had no sealer around it, and the various instructions I've seen make no mention of any.
With the top half-up I slowly layed a bean of flowable silicon along the front-edge of that aluminum strip. The silicon slowly made a nice secondary seal along the strip, as well as filling any voids between the roofing material and the aluminum strip.
Whether or not this solves all the header-rail leaks or not remains to be seen. The silicon did flow into the cracks, and once the top is clamped down with the rubber seal in place I can only imagine that the silicon can only compliment the rubber.
On a positive note:
* Except for a drop here and there near the back, I had no appreciable leaks around the windows at all.
* Using the stock, available weather seals I had not even a single drop of water in the trunk. Previously I'd replaced the stock washers on the luggage rack with rubber lined washers that compress a rubber seal against the trunk when tightened. I also sealed the MG emblem with heavy silicon by putting a thick drop on each hole before lowering the emblem in place, then smeared what was left around posts that stick into the trunk area, capping them off with fuel line to make it look "finished".