Normally on these models, the l/h side exhaust (viewed from the rear) - has a small rubber stopper fitted under the exhaust, that the centre-stand sits up against with spring tension when in the 'up' position - this is what stops the c/stand from rubbing on the chain.
When the l/h side exhaust is gone - because a r/h exit 4-1 has been fitted - what you need to do is fabricate a small length of steel that bolts under the pillion peg and drops vertically with enough length to stop the centrestand touching the chain. I have made up a few of these over the years for Z1's etc with exactly the same problem. Even had 1 of them chromed !!

Normally a short length (start with 150 mm and reduce as you need) of 25mm x 2mm will do the trick. They look a bit naff unpainted, the other option is to use a much shorter length fitted closer to where the c/stand pivots ?
The brakes......hmmm. What size piston is in the VFR m/c ? It should be stamped or cast somewhere, usually on the bottom. It is probably a 5/8th (16mm) piston ?
There is another way to bleed the air out of the calipers, this has always worked for me. Take off 1 caliper, get a small G-clamp, remove both pads then wind the G-clamp *through* the hole where the inner (floating) pad is normally fitted. The outside (fixed) part of the G-clamp sits on the outer side of the caliper.
Just wind in slowly when the G-clamp touches the piston, and make sure it is centred on the piston. Wind the clamp in until the piston bottoms out.
You need to have the m/c cap off when you do this, and also keep a close eye on the brake fluid level.......keep some rags handy

you will need to soak up the excess brake fluid pushed back up the line.
Once the piston in 1 caliper has bottomed out, unwind the clamp and bolt the caliper back onto the forkleg with the pads fitted. Repeat this procedure on the other caliper and then re-fit the pads and bolt the caliper back up to the forkleg.
Go back up to the m/c, and start pumping the lever slowly. Add brake fluid as you need.
What you will have done, is bleed every tiny bit of air out the back of the pistons in each caliper. You *should* find that after a few pumps on the brake lever, you build up pressure very quickly.
This should get you the best pressure possible. One thing to remember - if the brake lines are still the OEM rubber lines you lose a lot of pressure as the old rubber lines will flex internally. Braided steel lines will fix this, or you could take the old lines to a brake shop and get them to make you up some new ones with the same fittings - these will be almost as good as braided s/steel lines but retain the old-school look.....
Keep up the good work