My exhaust pipe to muffler clamp seems to become loose on a regular basis....just me?
Also, does everyone have the gasket at this point also? Does anyone not use one? I have been using some flattened out copper pipe, but the muffler still seems to become loose.

The OEM gasket was made out of pixilated fairy dust sometimes referred to as Mica. You had to be extremely careful when installing these, as any bump or misalignment resulted in the fairies bid for freedom. These gaskets had to be installed correctly preferably with an assistant to assure alignment. The gasket needed to be placed over the header pipe slightly protruding this needed to be carefully slightly pushed in towards the centre. Then the muffler is carefully pushed in and over the header pipe and gasket, and tightened. 

These gaskets were at one time extremely expensive I was quoted $50.00 Au. I and others have tried various methods to stop the leaks. I've tried five types of gasket cement, muffler bandage, beer cans, strips of copper, brass, aluminium and wound stainless steel wire. All have worked to some extent but eventually failed. There is however a cure on the horizon. 
Regards Martin.

A cure on the horizon?  

A new reusable gasket is in the process of being patented. And it works, I and a few others are running prototypes.
Regards Martin.

Use an exhaust sealant between the headers and muffler, or buy one of of the gaskets to which Martin referred.

Good stuff!
The other issue was the muffler coming loose. Is this a common issue?

I've put Kopper Kote on mine to prevent galling and it has never come loose. You might want to check the condition of the exhaust hanger bracket. If the rubber has parted ways with the metal it could contribute to vibration. This could then lead to the muffler moving and loosening off.
Regards Martin.

I failed the MOT because of a leaky exhaust at the clamp holding the silencer to the exhaust pipes. This problem seems to run on for me. I made a gasket out of some roofers lead I had, but still doesn't seem to have worked. Also, the vibration dampers holding the battery tray had worn and split, so the rear reservoir had migrated over to the footrest bracket and developed a hairline crack...another fail! All the reservoirs are old and brittle now, so I'm getting a K100 one and fabricating a bracket to mount it on...Faffff!!!!

Any K reservoir is now old and prone to cracking. Get an aftermarket one from ebay (yes!) and a length of new hydraulic hose. Mount the reservoir on a bracket bolted behind the top footrest hanger bolt. Saves having to remove the battery/drain the hydraulic system if you need to remove the footrest hanger.

The battery tray anti-vibration mounts are another story; either a Mills & Boon romance or a Stephen King nightmare novel. It depends. I've had both. Try removing them; it's an M6 thread in the gearbox and if you are really lucky, they will come out in a rusty lump leaving the threads intact (the threads will need cleaning). Go to ebay and get a set of 20x20x6mm thread male-male anti-vibration mounts and cut down to suit. Use copious quantities of copaslip when winding them in.

If the rubber tears off the mushroom, I don't see any way of proceeding without getting the gearbox out. Clean all the remaining rubber crap off the mushrooms, then cut a slot across each one to take an impact driver bit. Get as much heat around each mushroom as you can before blattering the bejesus out of the bugger. If it starts to unscrew, great. Rinse and repeat with the anti-vib mounts as above.

Now to the Stephen King nightmare novel(s). Chances are that one or more will just rotate which is fine (to a point); a bit of penetrating oil in there and you should be able to lever it out with a screwdriver. With luck, a shitty lump of rust will come out and you will be able to clean the threads with a 6mm tap. But: in this scenario the threads in the gearbox may have been destroyed. Three of those threads go right through the casting but the forward-right one is a blind thread about 6mm deep. Drill and tap the three through holes to 8mm. The fourth (blind) hole I'm going to leave to you. If you're skilled with the hand tools you may be able to thread it with a modified bottoming tap (which is what I did).

There is not enough room in the battery tray recesses to successfully use an 8mm full nut. Get a set of 20x20x8mm thread (or 30x20x8mm - the 20mm height is the critical bit) male-female anti-vibration mounts. Also buy four 10mm long x 8mm thread button-head allen screws to hold the battery tray down. If you haven't threaded the blind hole then just cut the male thread off one mount. Drill the battery tray holes out to 8mm.

The very worst scenario (and I've been here too and I really don't want to go back) is the mushroom shearing off the thread. If you have a pillar drill you should be able to drill them out but I spent hours (well, about twenty minutes) figuring out how to level up the gearbox and hold it securely. A handheld drill is a total no-go. Call in the professionals and go up to 8mm threads...

For the exhaust, PM me with your address and I'll send you a tube of Delkovic exhaust paste.

My mounts broke off at the mushrooms. I bought some from eBay and removed the mushrooms from one end. I then used sugrue glue and glued the rubbers onto the mushrooms on the gearbox. They needed time to set but now are strong enough to hold the tray tightly. Total cost was 30 minutes and £10

That's a possibility... I'm a bit 'old skool' and don't trust gluing metal to rubber when the end result has to carry any form of load.

Yeah...worst case scenario for me...mushrooms have sheared off, and all the studs are stuck! Battery tray held on with cable ties at the moment, but it doesn't make me happy!
On the exhaust clamp front...flatened out some 22mm copper tube to make a copper gasket, then sealed it also with some exhaust paste and glass wool. Seems to be working very well at the moment. The slight pop occasionally could be valves (never done em), air intakes or TPS?

usually the rubber battery tray buffers sheer off the mounting stud ...as mentioned before

use a flat blade sacrificial screwdriver to bite into the edge of the base of the rubber mount (metal bit )  with a hammering action in the direction of unscrewing …
worked for me a couple of times so far on all 4 mounts on each of 2 gearboxes
which then cleanly screwed out

have seen and has happened to me ... the threaded gearbox mount holes reamed out of thread section by loosly tightened buffers vibrating around within the thread section for about 10mm deep

for three of the mounts  just tap through the gearbox casing with a 6 mm tap  and select the buffers mentioned on ebay with slightly longer threaded studs ...the top stud can be cut to suit the tray and fixing nut .

good luck