Form 5498 can only be filed by an IRA custodian, and pertains to IRA contributions, not distributions, so your mention of Form 5498 doesn't make sense. Do you mean Form 5329, not Form 5498?
You claim the penalty exception by filing Form 5329, not by changing the distribution code on the Form 1099-R. On such a Form 5329 you would show the amount on line 2 with code 03.
When filing Form 5329 to claim a disability exception to the early-distribution penalty, you must provide to the IRS documentation (a letter) from a physician that supports your assertion that you are disabled. From page 25 of IRS Pub 590-B:
Disabled. If you become disabled before you reach age 59½, any distributions from your traditional IRA because of your disability aren't subject to the 10% additional tax.
You are considered disabled if you can furnish proof that you can't do any substantial gainful activity because of your physical or mental condition. A physician must determine that your condition can be expected to result in death or to be of long, continued, and indefinite duration.
The same applies to distributions from employer plans.
