Vespa, I seem to remember your post on another board about receiving Mk2 pillar covers for your Mk1.
MGRestorer, you are correct, the rear glass has to come out to install the pillar covers, side windows also. Fitting front and rear window glass to a Mini is different from what you normally do with other cars. The "string method" does not work well and can damage those new pillar covers.
Fit the rubber seal to the body opening and tape it in place. If you are using bulk seal material you need to cut it "long" and make sure the ends butt up against each other. Then fit the glass to the rubber seal. Start by resting the glass into the bottom of the seal. Use a plastic spatula or plastic putty knife to lever the rubber up over the glass while pushing the glass down and in. A little K-Y Jelly will make this easier. Work up each side, then across the top.
When the glass is in, you need to fit the lock strip. Make or buy the tool. Do not use a screwdriver or you are likely to hurt yourself or the new paint. Once again, K-Y Jelly will help you get the lockstrip in. As with the rubber seal, cut the lockstrip long so its ends press firmly against each other. Be sure to fit the finishing clip to the lockstrip before pressing the last bit of lockstrip in place.