You don't need to worry about doing anything with the uppers - leave them be.
If you're adamant about not blowing some dollars for even used aftermarket lowers, then I guess you can just weld some plate intoonto the stock ones. You want to heatsink for the bushings and be sure to sleeve the bolts for compression.
Why not just splurge on some better lowers. You're even cheaper than me!
BTW, sounds like you scored well on a 30k mile FLT there.
\'96SS SOB: SSRI, Herter Tune, Tri-Y II, SLP SS, 3000 Edge, F/HO bars, METCO extendeds and CV MMC, Bilsteins, currently Vredestein Ultrac Sessanta (315/35 rear)
\'96FWB BUW-Butt Ugly White: SS Bars, METCO LCAs, Koni Reds, PowerTrax No-Slip