I know a few who have lowered their FJRs and none have reported serious issues with handling.
I wouldn't think you'd have a problem with dragging hard parts unless you are really aggressive while cornering.
Once you modify the seat ($$) and if that doesn't work it will cost you more ($$) to return it to OEM unless you buy a second seat to have modified. I know that Kasey rides an '03 and had the front of her seat modified (IIRC, lowered an inch or so).
Links would certainly be a cheaper method and easily changed back of you're not happy. I would think you might find a used set, perhaps on ebay.
If you do go with links, the problems mentioned above will apply: The kickstand will need to be modified (either bent "out" or shortened) and putting the bike on the center stand may require help.
In the interest of clarity, especially for someone new...
Links will not be a cheaper method. Here's why:
1) the links themselves will cost 50? a 100? whatever. Yes they could be resold, possibly.
2) lowering the kickstand (and centerstand) is going to cost quite a bit. And to go back to oem, if needed, not an inexpensive option.
3) if you lower in the back (links), many will recommend you lower the tubes in the front by the same amount, to keep the suspension geometry the same. this can be "undone" easily though.
4)
NONE of these things are done by someone without some mechanical ability. NOTE: yer paying money for someone else to do that.
Seat Modification:
1) Spencer (for one) is an inexpensive option. His modifications will
improve the seat. It's highly unlikely you would ever want to go back to OEM, I mean, the seat has been lowered and modified for long distance. If you want even further adjustments than yes, it would cost more. But generally, the seat is a big help, but some may need even further help.
2) so now, you keep the seat (of course, it's an improvement), and you use smaller lowering links.
If necessary!
Start out with the seat. It's inexpensive and will be an improvement, no matters what. You can take the seat on and off, you don't have to pay someone else for anything but the modification of the seat.
Go from there...