if any of the ports only have 1 bolt they 'will' leak at some point in the future. i've 'slotted' all 4 port flanges before so all the bottom bolts can be started then slip the header down onto them.
neil.
A couple ports have 1 upper bolt with at least a side bolt, most have upper and 2 side bolts. 2 ports upper, lower and a side.
Not really the greatest setup with an upper and a side. I'd really recommend making every port have 2 opposing bolts as a minimum.
So back to your original question, no issue at all raising the engine up, go for it. If you are 100% sure there are no leaks now, put a little anti-seize on the new bolts, and tighten them, then retighten all the rest. It may not be a fun day, but you can lift the whole front of the engine a bit, or one motor mount at a time and rock it, multiple options.
If I did it, on the pairs that weren't opposing bolts, I think I might loosen those, then tighten evenly. Depends how sure I was that there was no leak, but honestly, they all probably loosened up after a few heat cycles anyway, likely don't need to. So, when you get the other ones in, evenly tighten them all again
Some tips, in no specific order.
1 - Don't accept failure, there is a way to get to the bolts
2 - Find as many 7/16 wrenches as you can, they all have different angles. Don't use crappy wrenches that will slip.
3 - A good ratchet and flex socket can be your friend
4 - your other friend could be 1/4 inch drive stuff but usually not enough power for final tightening
5 - Tighten pairs evenly in the least, all tightened in steps evenly is best. Don't over torque, but don't stop until you feel your inside voice say "that ain't going nowhere"
Writing a book here, but whether a Mustang, Fairlane or truck, there are always tough bolts. What I do is anti-seize every bolt, tighten evenly, fire the car. Then when hot I go back long sleeves and gloves (or just tough it out) and snug every one again, they will be loose.
Last comment, he (the tuner) may not get every bolt the way he wants it, some won't fit by tight turns of the pipe sometimes, but I am guessing he either hears a leak, or uses an A/F sensor to tune and knows an exhaust leak will change numbers. Now is the time to get it right before it burns a gasket