diff --git a/scripts/paperclip-commit-metrics.ts b/scripts/paperclip-commit-metrics.ts
index 5f989ca1..8a648afa 100644
--- a/scripts/paperclip-commit-metrics.ts
+++ b/scripts/paperclip-commit-metrics.ts
@@ -436,6 +436,9 @@ async function searchWindow(
 
   for (let page = 2; page <= pageCount; page += 1) {
     const response = await searchPage(client, options, start, end, page, 100);
+    if (response.incomplete_results) {
+      throw new Error(`GitHub returned incomplete search results for window ${windowKey} on page ${page}`);
+    }
     ingestSearchItems(cache, response.items, shas);
   }
 
@@ -509,7 +512,7 @@ function sortFilteredShas(cache: CacheFile, shas: string[]): string[] {
 }
 
 function formatQueryDate(value: Date): string {
-  return value.toISOString().replace(".000Z", "Z");
+  return new Date(Math.floor(value.getTime() / 1000) * 1000).toISOString().replace(".000Z", "Z");
 }
 
 function ingestSearchItems(cache: CacheFile, items: SearchCommitItem[], shas: Set<string>) {
@@ -847,6 +850,14 @@ class GitHubClient {
         return (await response.json()) as T;
       }
 
+      const retryAfter = response.headers.get("retry-after");
+      if ((response.status === 403 || response.status === 429) && retryAfter) {
+        const waitMs = Math.max(Number.parseInt(retryAfter, 10) * 1000, 1_000);
+        console.error(`GitHub secondary rate limit hit for ${pathname}; waiting ${Math.ceil(waitMs / 1000)}s...`);
+        await sleep(waitMs);
+        continue;
+      }
+
       const remaining = response.headers.get("x-ratelimit-remaining");
       const resetAt = response.headers.get("x-ratelimit-reset");
       if ((response.status === 403 || response.status === 429) && remaining === "0" && resetAt) {